| lsdeluxe |
x86_64 |
1.1.2 |
2024-05-24 |
1.1.2* |
lsd |
ls, lsd |
utilities |
link |
|
| bat |
x86_64 |
0.24.0 |
2024-05-24 |
0.24.0* |
bat |
cat, bat |
utilities |
link |
|
| fd |
x86_64 |
10.1.0 |
2024-05-24 |
10.1.0* |
fd |
fd, find |
utilities |
link |
|
| bbmap |
x86_64 |
39.33 |
2024-05-24 |
39.6, 39.8, 39.33* |
bbmap.sh, ... |
bbmap, bbduk, quality-control, QC, omics |
life sciences |
link |
link |
| blast |
x86_64 |
2.16.0 |
2024-05-24 |
2.15.0, 2.16.0* |
blastn, ... |
blast, ncbi, alignment |
life sciences |
link |
link |
| bwa |
x86_64 |
0.7.19 |
2024-05-25 |
0.7.18, 0.7.19* |
bwa |
BWA, Burrow-Wheeler Aligner for short-read alignment |
life sciences |
link |
link |
| minimap2 |
x86_64 |
2.30 |
2024-05-25 |
2.28, 2.29, 2.30* |
minimap2, ... |
minimap2, versatile pairwise aligner for genomic and spliced nucleotide sequences |
life sciences |
link |
link |
| diamond |
x86_64 |
2.1.11 |
2024-06-10 |
2.1.9*, 2.1.11 |
diamond |
diamond, blast, alignment |
life sciences |
link, link |
link |
| iqtree |
x86_64 |
3.0.1 |
2024-06-10 |
2.3.4, 2.4.0, 3.0.1* |
iqtree, ... |
IQ-TREE, Efficient phylogenomic software by maximum likelihood |
life sciences |
link |
link |
| ripgrep |
x86_64 |
14.1.1 |
2024-06-11 |
14.1.1* |
rg |
rg, ripgrep |
utilities |
link |
|
| vsearch |
x86_64 |
2.28.1 |
2024-06-12 |
2.28.1* |
vsearch |
vsearch, alignment |
life sciences |
link |
link |
| seqkit |
x86_64 |
2.8.2 |
2024-06-12 |
2.8.2* |
seqkit |
seqkit, conversion, utility |
life sciences |
link |
link, link |
| sina |
x86_64 |
1.7.2 |
2024-06-12 |
1.7.2* |
sina |
sina, alignment, 16S |
life sciences |
link, link |
link |
| tldr |
x86_64 |
3.2.0 |
2024-06-12 |
3.2.0* |
tldr |
tldr, manpage |
utilities |
link, link |
|
| fasttree |
x86_64 |
2.1.11 |
2024-06-12 |
2.1.11* |
fasttree, ... |
fasttree, phylogeny, phylogenetics |
life sciences |
link |
link, link |
| trimal |
x86_64 |
1.5.0 |
2024-06-12 |
1.4.1, 1.5.0* |
readal, ... |
trimAl, automated alignment trimming in large-scale phylogenetic analyses |
life sciences |
link |
link |
| nf-core |
x86_64 |
3.3.2 |
2024-06-12 |
2.14.1, 3.0.2, 3.2.0, 3.3.2* |
nf-core |
nf-core, community-curated bioinformatics pipelines |
life sciences |
link |
link |
| blobtools |
x86_64 |
1.1.1 |
2024-06-13 |
1.1.1* |
blobtools |
blobtools, QC, quality control |
life sciences |
link, link |
link, link |
| cafe |
x86_64 |
5.1.0 |
2024-06-18 |
5.1.0* |
cafe5 |
cafe, cafe5, phylogenetics |
life sciences |
link |
link |
| earlgrey |
x86_64 |
4.3.0 |
2024-06-18 |
4.3.0* |
earlGrey, ... |
earlgrey, earlGrey, repeats, transposable elements |
life sciences |
link |
link, link |
| htseq |
x86_64 |
2.0.5 |
2024-06-18 |
2.0.5* |
htseq-count, ... |
HTSeq, htseq, htseq-count, RNA-Seq |
life sciences |
link |
link |
| samtools |
x86_64 |
1.22.1 |
2024-06-18 |
1.20, 1.3, 1.21, 1.18, 1.22.1* |
ace2sam, ... |
samtools, Tools for dealing with SAM, BAM and CRAM files |
life sciences |
link |
link |
| bedtools |
x86_64 |
2.31.1 |
2024-06-18 |
2.31.1* |
bedtools, ... |
bedtools, gff, annotation, features, omics |
life sciences |
link, link |
link |
| busco |
x86_64 |
5.8.3 |
2024-06-18 |
5.7.1, 5.8.1, 5.8.3* |
busco, ... |
BUSCO, genome quality control, QC |
life sciences |
link |
link |
| stringtie |
x86_64 |
2.2.3 |
2024-06-19 |
2.2.3*, 2.2.1 |
stringtie, ... |
stringtie, RNA-Seq, omics |
life sciences |
link, link |
link |
| trimmomatic |
x86_64 |
0.39 |
2024-06-19 |
0.39* |
trimmomatic |
trimmomatic, trimming, qc, omics |
life sciences |
link, link |
link |
| hmmer |
x86_64 |
3.4 |
2024-06-19 |
3.4* |
hmmscan, ... |
hmmer, hmm, motif finding |
life sciences |
link, link |
link |
| pybiolib |
x86_64 |
1.1.2184 |
2024-06-19 |
1.1.2184* |
biolib |
biolib |
utilities |
link |
|
| picard |
x86_64 |
3.1.1 |
2024-06-19 |
3.1.1* |
picard |
picard |
utilities |
link, link |
link |
| hyphy |
x86_64 |
2.5.62 |
2024-06-19 |
2.5.62* |
hyphy, ... |
hyphy, phylogenetics |
life sciences |
link, link |
|
| transdecoder |
x86_64 |
5.7.1 |
2024-06-19 |
5.7.1* |
TransDecoder.LongOrfs, ... |
transdecoder, RNA-Seq, omics |
life sciences |
link |
link |
| viennarna |
x86_64 |
2.6.4 |
2024-06-19 |
2.6.4* |
RNAfold, ... |
ViennaRNA, RNA, secondary structure, omics |
life sciences |
link |
link |
| trnascan-se |
x86_64 |
2.0.12 |
2024-06-24 |
2.0.12* |
EukHighConfidenceFilter, ... |
trnascan, trnascan-se, tRNA, annotation |
life sciences |
link, link |
link |
| barrnap |
x86_64 |
0.9 |
2024-06-24 |
0.9* |
barrnap |
barrnap, rRNA, annotation |
life sciences |
link |
|
| orthofinder |
x86_64 |
3.0.1b1 |
2024-06-24 |
2.5.5, 3.0.1b1* |
orthofinder, ... |
OrthoFinder, Phylogenetic orthology inference for comparative genomics |
life sciences |
link |
link |
| rattler-build |
x86_64 |
0.31.1 |
2024-06-24 |
0.31.1* |
rattler-build |
rattler-build, build |
utilities |
link, link |
|
| conda-recipe-manager |
x86_64 |
0.2.0 |
2024-06-24 |
0.2.0* |
conda-recipe-manager |
conda-recipe-manager, conda, build |
utilities |
link |
|
| spades |
x86_64 |
4.1.0 |
2024-06-24 |
4.0.0, 4.1.0* |
coronaspades.py, ... |
SPAdes, Genome assembler |
life sciences |
link |
link |
| quast |
x86_64 |
5.2.0 |
2024-06-26 |
5.2.0* |
quast, ... |
quast, QC, quality-control, assembly, omics |
life sciences |
link, link |
link |
| GeneMark-ES |
x86_64 |
4.71 |
2024-06-26 |
4.71* |
gmes_petap.pl |
GeneMark-ES, gmes_petap.pl, annotation, omics |
life sciences |
link |
link |
| mrbayes |
x86_64 |
3.2.7 |
2024-06-26 |
3.2.7* |
mb, ... |
MrBayes, mrbayes, Bayesian stats, MCMC, phylogenetics |
life sciences |
link, link |
link |
| mafft |
x86_64 |
7.526 |
2024-06-26 |
7.526* |
mafft, ... |
mafft, alignment, msa |
life sciences |
link |
link |
| muscle |
x86_64 |
5.3 |
2024-06-26 |
5.1, 5.3* |
muscle |
Muscle, Multiple sequence and structure alignment |
life sciences |
link |
link |
| orthomcl |
x86_64 |
2.0.9 |
2024-06-26 |
2.0.9* |
orthomclAdjustFasta, ... |
orthomcl, orthology, orthogroups, omics |
life sciences |
link |
link |
| pal2nal |
x86_64 |
14.1 |
2024-06-27 |
14.1* |
pal2nal.pl |
pal2nal, alignment, msa, conversion |
life sciences |
link |
link |
| ClonalFrameML |
x86_64 |
1.13 |
2024-06-27 |
1.13* |
ClonalFrameML |
ClonalFrame, ClonalFrameML, recombination, omics, phylogenetics |
life sciences |
link, link |
link |
| CheckM2 |
x86_64 |
1.0.2 |
2024-06-27 |
1.0.2* |
checkm2 |
CheckM, CheckM2, quality control, QC, omics |
life sciences |
link |
|
| CheckM |
x86_64 |
1.2.3 |
2024-06-27 |
1.2.3* |
checkm |
CheckM, quality control, QC, omics |
life sciences |
link, link |
link |
| qualimap |
x86_64 |
2.3 |
2024-06-27 |
2.3* |
qualimap |
qualimap, alignment, quality control, QC, omics |
life sciences |
link |
link |
| gffread |
x86_64 |
0.12.7 |
2024-06-27 |
0.12.7* |
gffread |
gffread, conversion tool, gff, omics |
utilities |
link, link |
link |
| alistat |
x86_64 |
1.15 |
2024-06-27 |
1.15* |
alistat |
alistat, phylogenomics, msa, QC, quality control |
life sciences |
link |
link |
| get_pangenes |
x86_64 |
20240627 |
2024-06-27 |
20240627* |
get_pangenes.pl, ... |
get_pangenes, comparative genomics, pangenomes |
life sciences |
link |
link, link |
| kallisto |
x86_64 |
0.50.1 |
2024-06-27 |
0.50.1* |
kallisto |
kallisto, RNA-Seq, transcriptomics |
life sciences |
link |
link |
| hisat2 |
x86_64 |
2.2.1 |
2024-06-27 |
2.2.1* |
extract_exons.py, ... |
hisat2, RNA-Seq, transcriptomics |
life sciences |
link |
link |
| vcftools |
x86_64 |
0.1.17 |
2024-06-27 |
0.1.16, 0.1.17* |
vcftools, ... |
VCFtools, tools for working with VCF files |
life sciences |
link |
link |
| gatk4 |
x86_64 |
4.5.0.0 |
2024-06-28 |
4.5.0.0* |
gatk |
gatk, SNPs, variant calling, variant analysis |
life sciences |
link, link |
link, link, link |
| STAR |
x86_64 |
2.7.11b0 |
2024-06-28 |
2.7.11b0* |
STAR, ... |
STAR, RNA-Seq, transcriptomics |
life sciences |
link, link, link |
link |
| cutadapt |
x86_64 |
4.9 |
2024-06-28 |
4.9* |
cutadapt |
cutadapt, QC, quality control, omics |
life sciences |
link, link |
link |
| flye |
x86_64 |
2.9.4 |
2024-06-28 |
2.9.4* |
flye, ... |
flye, assembly, long reads, omics |
life sciences |
link |
link, link |
| RAxML |
x86_64 |
8.2.13 |
2024-06-28 |
8.2.13* |
raxmlHPC, ... |
RAxML, phylogenetics |
life sciences |
link |
link |
| raxml-ng |
x86_64 |
1.2.2 |
2024-06-28 |
1.2.2* |
raxml-ng, ... |
raxml-ng, RAxML, phylogenetics |
life sciences |
link, link |
link |
| beast |
x86_64 |
1.10.4 |
2024-06-28 |
1.10.4* |
beast, ... |
BEAST, MCMC, Bayesian stats, phylogenetics |
life sciences |
link, link |
link |
| paml |
x86_64 |
4.10.7 |
2024-06-28 |
4.10.7* |
baseml, ... |
paml, evolution, phylogenetics |
life sciences |
link |
link |
| kofamscan |
x86_64 |
1.3.0 |
2024-06-28 |
1.3.0* |
kofam_scan |
kofamscan, annotation, KEGG, KO, KOFAM |
life sciences |
|
|
| isescan |
x86_64 |
1.7.2.3 |
2024-06-28 |
1.7.2.3* |
isescan.py |
isescan, insertion elements, mobile genetic elements, annotation |
life sciences |
link |
link |
| jq |
x86_64 |
1.7.1 |
2024-06-28 |
1.7.1* |
jq |
jq, json |
utilities |
link |
|
| yq |
x86_64 |
3.4.3 |
2024-06-28 |
3.4.3* |
yq, ... |
yq, yaml |
utilities |
link |
|
| ncbi-datasets |
x86_64 |
16.22.1 |
2024-07-05 |
16.22.1* |
datasets, ... |
ncbi-datasets, datasets, genome download |
utilities |
link, link, link |
|
| seqtk |
x86_64 |
1.4 |
2024-07-11 |
1.4* |
seqtk |
seqtk, utility, conversion |
life sciences |
link |
|
| fastq_utils |
x86_64 |
0.25.2 |
2024-07-11 |
0.25.2* |
fastq_info, ... |
fastq_utils, utility, FASTQ, QC |
life sciences |
link |
|
| fastqc |
x86_64 |
0.12.1 |
2024-07-11 |
0.12.1* |
fastqc |
fastqc, utility, QC |
life sciences |
link |
|
| nextflow |
x86_64 |
25.4.6 |
2024-07-11 |
24.4.3, 24.10.4, 25.4.6* |
nextflow |
nextflow, A DSL for data-driven computational pipelines |
life sciences |
link |
link |
| multiqc |
x86_64 |
1.27.1 |
2024-07-11 |
1.23, 1.27.1* |
multiqc |
MultiQC, Aggregate results from bioinformatics analyses across many samples into a single report |
life sciences |
link |
link |
| R |
x86_64 |
4.4.2 |
2024-07-12 |
4.3.3, 4.4.2 |
R, ... |
R, jupyter |
languages |
link |
|
| btop |
x86_64 |
1.3.2 |
2024-07-12 |
1.3.2* |
btop |
btop, top |
utilities |
link |
|
| eggnog-mapper |
x86_64 |
2.1.12 |
2024-07-16 |
2.1.12* |
emapper.py, ... |
eggnog-mapper, annotation, omics |
life sciences |
link |
link, link |
| metaphlan |
x86_64 |
4.1.1 |
2024-07-17 |
4.1.1* |
metaphlan, ... |
metaphlan, metagenomics |
life sciences |
link |
link |
| trinity |
x86_64 |
2.15.2 |
2024-07-23 |
2.15.1, 2.15.2* |
Trinity, ... |
Trinity, assembly, RNA-Seq |
life sciences |
link |
link |
| bioconvert |
x86_64 |
1.1.1 |
2024-07-23 |
1.1.1* |
bioconvert |
bioconvert, conversion tool |
utilities |
link |
|
| bakta |
x86_64 |
1.9.4 |
2024-07-23 |
1.9.4* |
bakta, ... |
bakta, annotation |
life sciences |
link |
link, link |
| humann |
x86_64 |
3.9 |
2024-07-26 |
3.9* |
humann, ... |
humann, metagenomics |
life sciences |
link |
link |
| kneaddata |
x86_64 |
0.12.2 |
2024-07-26 |
0.12.0, 0.12.2* |
kneaddata, ... |
kneaddata, QC, metagenomics, host removal |
life sciences |
link, link |
|
| kraken2 |
x86_64 |
2.14 |
2024-07-26 |
2.1.3, 2.14*, 2.1.6 |
k2, ... |
kraken2, metagenomics |
life sciences |
link, link |
link |
| qiime2 |
x86_64 |
2024.5 |
2024-08-06 |
2024.5* |
qiime |
qiime2, qiime, metagenomics, 16S |
life sciences |
link |
|
| EDTA |
x86_64 |
20240806 |
2024-08-06 |
20240806* |
EDTA.pl, ... |
EDTA, TE, omics, transposable elements, annotation |
life sciences |
link |
link, link, link |
| stacks |
x86_64 |
2.65 |
2024-08-08 |
2.65* |
denovo_map.pl, ... |
Stacks, RAD-seq, population genetics |
life sciences |
link |
link |
| structure |
x86_64 |
2.3.4 |
2024-08-08 |
2.3.4* |
structure |
Structure, population genetics |
life sciences |
link |
link, link |
| sra-tools |
x86_64 |
3.1.1 |
2024-08-15 |
3.1.1* |
sratools, ... |
sra-tools, NCBI |
utilities |
link |
|
| skani |
x86_64 |
0.2.2 |
2024-08-15 |
0.2.2* |
skani |
skani, ANI, average nucleotide identity |
life sciences |
link, link |
link |
| nanoplot |
x86_64 |
1.43.0 |
2024-08-16 |
1.43.0* |
NanoPlot |
nanoplot, long read, nanopore, QC |
life sciences |
link |
link |
| pilon |
x86_64 |
1.24 |
2024-08-16 |
1.24* |
pilon |
pilon, long read, nanopore, assembly |
life sciences |
link |
link |
| genomescope2 |
x86_64 |
2.0.1 |
2024-08-16 |
2.0.1* |
genomescope2 |
genomescope2, omics, QC |
life sciences |
link |
link |
| disperseNN2 |
x86_64 |
0.0.7 |
2024-08-16 |
0.0.7* |
disperseNN2 |
disperseNN2 |
life sciences |
link |
link |
| fineradstructure |
x86_64 |
0.3.2 |
2024-08-16 |
0.3.2* |
finestructure, ... |
fineRADstructure, RADpainter, population genetics, population structure |
life sciences |
link |
link |
| admixture |
x86_64 |
1.3.0 |
2024-08-16 |
1.3.0* |
admixture |
admixture, ancestral reconstruction, SNPs |
life sciences |
link |
link |
| faststructure |
x86_64 |
1.0 |
2024-08-16 |
1.0* |
structure.py, ... |
fastSTRUCTURE, population structure, population genetics, SNPs |
life sciences |
link |
link |
| bellerophon |
x86_64 |
1.0 |
2024-08-16 |
1.0* |
bellerophon |
bellerophon, assembly, scaffolding, Hi-C |
life sciences |
link, link |
|
| python-dotenv |
x86_64 |
1.0.1 |
2024-08-19 |
1.0.1* |
dotenv |
python-dotenv, configuration |
utilities |
link |
|
| direnv |
x86_64 |
2.34.0 |
2024-08-19 |
2.34.0* |
direnv |
direnv, configuration |
utilities |
link |
|
| gtdbtk |
x86_64 |
2.4.0 |
2024-08-20 |
2.4.0* |
gtdbtk |
gtdb, gtdbtk, omics, species classification |
life sciences |
link |
link, link |
| meme |
x86_64 |
5.5.6 |
2024-08-20 |
5.5.6* |
meme, ... |
meme, motif search, meme-suite |
life sciences |
link |
link, link |
| nodejs |
x86_64 |
22.11.0 |
2024-08-21 |
22.6, 22.11.0 |
node, ... |
node, nodejs, npm |
languages |
link |
|
| sregistry |
x86_64 |
0.2.39 |
2024-08-27 |
0.2.39 |
sregistry |
sregistry, singularity |
utilities |
link |
|
| mummer4 |
x86_64 |
4.0.0 |
2024-08-27 |
4.0.0* |
mummer, ... |
Mummer, Mummer alignment tool |
life sciences |
link |
link |
| nextpolish |
x86_64 |
1.4.1 |
2024-08-27 |
1.4.1* |
nextPolish, ... |
nextpolish, QC, assembly |
life sciences |
link, link |
link |
| augustus |
x86_64 |
3.5.0 |
2024-08-29 |
3.5.0* |
augustus, ... |
augustus, annotation |
life sciences |
link |
link |
| wfmash |
x86_64 |
0.20.0 |
2024-08-30 |
0.20.0* |
wfmash, ... |
wfmash, alignment, omics, whole genome alignment |
life sciences |
link |
link, link, link |
| rsem |
x86_64 |
1.3.3 |
2024-08-30 |
1.3.3* |
convert-sam-for-rsem, ... |
RSEM, RNA-Seq, quantification of gene and isoform expression |
life sciences |
link |
link |
| ribodetector |
x86_64 |
0.3.1 |
2024-08-30 |
0.3.1* |
ribodetector, ... |
RiboDetector, rRNA |
life sciences |
link |
link |
| smudgeplot |
x86_64 |
0.2.5 |
2024-08-30 |
0.2.5* |
smudgeplot.py, ... |
smudgeplot, Inference of ploidy and heterozygosity structure using whole genome sequencing data |
life sciences |
link |
link |
| interproscan |
x86_64 |
5.69 |
2024-08-30 |
5.59, 5.69* |
interproscan.sh |
InterProScan, Genome-scale protein function classification, gene annotation |
life sciences |
link |
link |
| repeatmasker |
x86_64 |
4.2.1 |
2024-08-30 |
4.1.5, 4.1.9, 4.2.1* |
DupMasker, ... |
RepeatMasker, screens DNA sequences for interspersed repeats and low complexity DNA sequences, repetitive elements |
life sciences |
link |
link |
| repeatmodeler |
x86_64 |
2.0.7 |
2024-08-30 |
2.0.5, 2.0.6, 2.0.7* |
BuildDatabase, ... |
RepeatModeler, de-novo repeat family identification and modeling, repetitive elements |
life sciences |
link |
link |
| sourmash |
x86_64 |
4.8.11 |
2024-09-03 |
4.8.11* |
sourmash |
sourmash, Quickly search, compare, and analyze genomic and metagenomic data sets |
life sciences |
link |
link |
| canu |
x86_64 |
2.3 |
2024-09-04 |
2.2, 2.3* |
canu, ... |
canu, assembly, long-read, omics |
life sciences |
link, link |
link, link |
| poplddecay |
x86_64 |
3.43 |
2024-09-06 |
3.43* |
PopLDdecay, ... |
PopLDDecay, population genomics, SNPs |
life sciences |
link |
link |
| fragpipe |
x86_64 |
20.0 |
2024-09-06 |
20.0* |
fragpipe, ... |
FragPipe, comprehensive analysis of shotgun proteomics data |
life sciences |
link |
link |
| plink |
x86_64 |
20240818 |
2024-09-06 |
20240818* |
plink |
plink, population genomics, SNPs, GWAS |
life sciences |
link, link |
link |
| plink2 |
x86_64 |
20240820 |
2024-09-06 |
20240820* |
plink2 |
plink2, population genomics, SNPs, GWAS |
life sciences |
link, link |
link |
| fastsimcoal |
x86_64 |
2.8 |
2024-09-06 |
2.8* |
fsc28 |
fastsimcoal, population genomics, evolution, recombination |
life sciences |
link, link |
link |
| angsd |
x86_64 |
0.940 |
2024-09-06 |
0.940* |
angsd, ... |
ANGSD, population genetics, omics |
life sciences |
link, link |
link |
| antismash |
x86_64 |
7.1.0 |
2024-09-10 |
7.1.0* |
antismash |
antiSMASH, antibiotics and Secondary Metabolite Analysis SHell |
life sciences |
link |
link |
| fastp |
x86_64 |
0.24.0 |
2024-09-10 |
0.23.4, 0.24.0* |
fastp |
fastp, ultra-fast FASTQ preprocessor QC adapters trimming filtering splitting |
life sciences |
link |
link |
| dsuite |
x86_64 |
0.5 |
2024-09-13 |
0.5* |
Dsuite, ... |
Dsuite, population genetics, admixutre, ABBA-BABA, omics |
life sciences |
link, link |
link, link |
| aria2 |
x86_64 |
1.37.0 |
2024-09-13 |
1.37.0*, 1.37.0* |
aria2c |
aria2, download-manager, tool |
utilities |
link |
link |
| snpeff |
x86_64 |
5.2 |
2024-09-16 |
5.2* |
snpEff |
SnpEff, Genetic variant annotation and effect prediction toolbox |
life sciences |
link |
link |
| get_homologues |
x86_64 |
3.7.1 |
2024-09-18 |
3.7.1* |
get_homologues.pl, ... |
GET_HOMOLOGUES, pan-genome analysis |
life sciences |
link |
link |
| spaln |
x86_64 |
3.0.6 |
2024-09-23 |
3.0.6* |
spaln, ... |
spaln, Genome mapping and spliced alignment of cDNA or amino acid sequences |
life sciences |
link |
link |
| julia |
x86_64 |
1.10.5 |
2024-09-24 |
1.10.5* |
julia |
julia |
languages |
link |
|
| ncdu |
x86_64 |
2.5 |
2024-09-24 |
2.5* |
ncdu |
ncdu |
utilities |
link |
|
| syri |
x86_64 |
1.7.0 |
2024-10-01 |
1.7.0* |
syri, ... |
SyRI, Synteny and rearrangement identifier between whole-genome assemblies |
life sciences |
link |
link |
| plotsr |
x86_64 |
1.1.1 |
2024-10-01 |
1.1.1* |
plotsr |
plotsr, plot synteny and structural rearrangements between genomes |
life sciences |
link |
link |
| idemuxcpp |
x86_64 |
0.3.0 |
2024-10-02 |
0.3.0* |
idemuxCPP |
idemuxCPP, demultiplex paired-end fastq files from QuantSeq-Pool |
life sciences |
link |
link |
| pyani |
x86_64 |
0.2.13.1 |
2024-10-07 |
0.2.13.1* |
pyani, ... |
pyani, ANI, omics |
life sciences |
link |
link |
| maker |
x86_64 |
2.31.9 |
2024-10-07 |
2.31.9* |
maker, ... |
maker, annotation, omics |
life sciences |
link |
link |
| getorganelle |
x86_64 |
1.7.7.1 |
2024-10-07 |
1.7.7.1* |
get_organelle_from_reads.py, ... |
GetOrganelle, assembly, eukaryotes, mitochondria |
life sciences |
link |
link |
| oatk |
x86_64 |
1.0 |
2024-10-08 |
1.0* |
oatk, ... |
Oatk, de novo assembly of complex plant organelle genomes using PacBio HiFi data |
life sciences |
link |
link |
| ragtag |
x86_64 |
2.1.0 |
2024-10-08 |
2.1.0* |
ragtag.py, ... |
RagTag, Tools for fast and flexible genome assembly scaffolding and improvement |
life sciences |
link |
link |
| snakemake |
x86_64 |
8.20.6 |
2024-10-09 |
8.20.6 |
snakemake |
snakemake, pipeline, python |
utilities |
link |
link |
| blat |
x86_64 |
469 |
2024-10-14 |
469* |
blat, ... |
blat, ucsc-blat, alignment |
life sciences |
link, link |
link |
| dos2unix |
x86_64 |
7.4.0 |
2024-10-14 |
7.4.0 |
dos2unix, ... |
dos2unix |
utilities |
link |
|
| pear |
x86_64 |
0.9.6 |
2024-10-14 |
0.9.6* |
pear, ... |
pear, read merger, omics |
life sciences |
link |
|
| phyluce |
x86_64 |
1.7.3 |
2024-10-15 |
1.7.3* |
phyluce_workflow, ... |
phyluce, illumiprocessor, QC, phylogenomics |
life sciences |
link |
link |
| samblaster |
x86_64 |
0.1.26 |
2024-10-16 |
0.1.26* |
samblaster |
samblaster, tool to mark duplicates and extract discordant and split reads from sam files |
life sciences |
link |
link |
| mifish |
x86_64 |
2.0.0 |
2024-10-17 |
2.0.0* |
mifish |
mifish, metabarcoding |
life sciences |
link |
link |
| nvitop |
x86_64 |
1.3.2 |
2024-10-17 |
1.3.2 |
nvitop |
nvitop, monitoring |
utilities |
link |
|
| idemux |
x86_64 |
0.1.6 |
2024-10-18 |
0.1.6* |
idemux |
idemux, demultiplex paired-end fastq files from QuantSeq Pool |
life sciences |
link |
link |
| glimmer |
x86_64 |
3.2 |
2024-10-22 |
3.2* |
glimmer3, ... |
glimmer, annotation |
life sciences |
link |
link |
| p7zip |
x86_64 |
16.2 |
2024-10-22 |
16.2* |
7z, ... |
7zip, p7zip |
utilities |
link |
|
| alphafold |
x86_64 |
20241029 |
2024-10-29 |
20241029 |
run_alphafold |
alphafold, gpgpu, protein folding |
life sciences |
link |
link |
| metamdbg |
x86_64 |
1.0 |
2024-10-30 |
1.0* |
metaMDBG |
MetaMDBG, lightweight assembler for long and accurate metagenomics reads |
life sciences |
link |
link |
| axe-demultiplexer |
x86_64 |
0.3.3 |
2024-11-01 |
0.3.3* |
axe-demux |
Axe, Rapid competitive read demulitplexer |
life sciences |
link |
link |
| liftoff |
x86_64 |
1.6.3 |
2024-11-04 |
1.6.3* |
liftoff |
Liftoff, accurate GFF3/GTF lift over pipeline |
life sciences |
link |
link |
| plass |
x86_64 |
5.0 |
2024-11-04 |
5.0* |
plass, ... |
Plass, PenguiN, sensitive and precise assembly of short sequencing reads |
life sciences |
link |
link |
| agat |
x86_64 |
1.4.1 |
2024-11-05 |
1.4.1* |
agat, ... |
AGAT, sensitive and precise assembly of short sequencing reads |
life sciences |
link |
link |
| duf |
x86_64 |
0.8.1 |
2024-11-07 |
0.8.1* |
duf |
duf, disk usage, df |
utilities |
link |
|
| miniprot |
x86_64 |
0.15 |
2024-11-08 |
0.13, 0.14, 0.15* |
miniprot |
Miniprot, Align proteins to genomes with splicing and frameshift |
life sciences |
link |
link |
| lifton |
x86_64 |
1.0.5 |
2024-11-08 |
1.0.5* |
lifton |
lifton, annotation, omics |
life sciences |
link |
link |
| currentNe |
x86_64 |
1.0.0 |
2024-11-08 |
1.0.0* |
currentNe |
currentNe, popgen |
life sciences |
link |
|
| liftofftools |
x86_64 |
0.4.4 |
2024-11-19 |
0.4.4* |
liftofftools |
LiftoffTools, toolkit to compare genes lifted between genome assemblies |
life sciences |
link |
link |
| taxonkit |
x86_64 |
0.18.0 |
2024-11-24 |
0.18.0* |
taxonkit |
taxonkit, utility, taxonomy |
life sciences |
link |
link |
| yahs |
x86_64 |
1.2.2 |
2024-11-25 |
1.2.2* |
yahs, ... |
YaHS, yet another Hi-C scaffolding tool |
life sciences |
link |
link |
| gfastats |
x86_64 |
1.3.9 |
2024-11-25 |
1.3.9* |
gfastats |
gfastats, genome assembly file manipulation |
life sciences |
link |
link |
| pcangsd |
x86_64 |
1.35 |
2024-11-26 |
1.35* |
pcangsd |
PCAngsd, pcangsd, omics, PCA |
life sciences |
link |
link, link, link |
| arcs |
x86_64 |
1.2.8 |
2024-11-26 |
1.2.8* |
arcs, ... |
arcs, scaffolding, long read, omics |
life sciences |
link |
link, link |
| dorado |
x86_64 |
0.7.2 |
2024-12-02 |
0.7.2* |
dorado |
Dorado, Oxford Nanopore Basecaller |
life sciences |
link |
link |
| sniffles |
x86_64 |
2.5.2 |
2024-12-03 |
2.5.2* |
sniffles |
Sniffles, Structural variation caller using third generation sequencing |
life sciences |
link |
link |
| manta |
x86_64 |
1.6.0 |
2024-12-03 |
1.6.0* |
configManta.py, ... |
Manta, Structural variant and indel caller for mapped sequencing data |
life sciences |
link |
link |
| tiddit |
x86_64 |
3.7.0 |
2024-12-03 |
3.7.0* |
tiddit |
TIDDIT, structural variant calling |
life sciences |
link |
link |
| cnvkit |
x86_64 |
0.9.12 |
2024-12-03 |
0.9.12* |
cnvkit.py |
CNVkit, Genome-wide copy number from high-throughput sequencing |
life sciences |
link |
link |
| canvas |
x86_64 |
1.35.1.1316 |
2024-12-04 |
1.35.1.1316* |
Canvas, ... |
Canvas, Copy number variant (CNV) calling from DNA sequencing data |
life sciences |
link |
link |
| pbtk |
x86_64 |
3.4.0 |
2024-12-04 |
3.4.0* |
bam2fasta, ... |
pbtk, PacBio Secondary Analysis Tools |
life sciences |
link |
link |
| mosdepth |
x86_64 |
0.3.10 |
2024-12-04 |
0.3.10* |
mosdepth |
mosdepth, fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing |
life sciences |
link |
link |
| ccmetagen |
x86_64 |
1.5.0 |
2024-12-04 |
1.5.0* |
CCMetagen.py, ... |
CCMetagen, metagenomics |
life sciences |
link |
link, link |
| flash2 |
x86_64 |
2.2.0 |
2024-12-04 |
2.2.0* |
flash2 |
flash2, flash, omics |
life sciences |
link |
link |
| sabre |
x86_64 |
1.0 |
2024-12-04 |
1.0* |
sabre |
sabre, demultiplex |
life sciences |
link |
|
| csvtk |
x86_64 |
0.32.0 |
2024-12-06 |
0.32.0* |
csvtk |
csvtk, tab-delimited, csv |
utilities |
link |
|
| signalp6-cpu |
x86_64 |
20241206 |
2024-12-06 |
20241206* |
signalp6-cpu |
signalp, signal peptides |
life sciences |
link, link |
link |
| umi_tools |
x86_64 |
1.1.6 |
2024-12-12 |
1.1.6* |
umi_tools |
UMI-tools, Modelling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy |
life sciences |
link |
link |
| medaka |
x86_64 |
2.1.0 |
2024-12-12 |
2.0.1, 2.1.0* |
medaka, ... |
Medaka, Sequence correction provided by ONT Research |
life sciences |
link |
link |
| emboss |
x86_64 |
6.6.0 |
2024-12-12 |
6.6.0* |
aaindexextract, ... |
EMBOSS, European Molecular Biology Open Software Suite |
life sciences |
link |
link |
| ltr_finder |
x86_64 |
1.7 |
2024-12-16 |
1.7* |
ltr_finder, ... |
LTR_Finder, efficient program for finding full-length LTR retrotranspsons in genome sequences |
life sciences |
link |
link |
| ltr_retriever |
x86_64 |
3.0.2 |
2024-12-19 |
3.0.1, 3.0.2* |
LTR_retriever, ... |
LTR_retriever, highly accurate and sensitive program for identification of LTR retrotransposons |
life sciences |
link |
link |
| psmc |
x86_64 |
0.6.5 |
2025-01-08 |
0.6.5* |
psmc, ... |
psmc, popgen, population size |
life sciences |
link |
link |
| gnuplot |
x86_64 |
5.4.10 |
2025-01-08 |
5.4.10* |
gnuplot |
gnuplot, plotting |
utilities |
link |
|
| cd-hit |
x86_64 |
4.8.1 |
2025-01-09 |
4.8.1* |
cd-hit, ... |
cd-hit, clustering, omics |
life sciences |
link |
link |
| edta |
x86_64 |
2.2.2 |
2025-01-09 |
2.2.2* |
EDTA.pl, ... |
EDTA, Extensive de-novo TE Annotator |
life sciences |
link |
link |
| mothur |
x86_64 |
1.48.2 |
2025-01-13 |
1.48.2* |
mothur, ... |
mothur, microbiome, 16S, metabarcoding |
life sciences |
link |
link |
| macs3 |
x86_64 |
3.0.2 |
2025-01-17 |
3.0.2* |
macs3 |
macs, MACS, MACS3, ChIP-Seq, transcript factor binding |
life sciences |
link |
link |
| ripgrep |
ppc64le |
14.1.1 |
2025-01-23 |
14.1.1* |
rg |
rg, ripgrep |
utilities |
link |
|
| sl |
x86_64 |
5.1 |
2025-01-24 |
5.1* |
sl |
sl |
utilities |
|
|
| entrez-direct |
x86_64 |
22.4 |
2025-01-24 |
22.4* |
efetch, ... |
entrez-direct, EDirect, NCBI |
life sciences |
link |
|
| nvim |
x86_64 |
0.10.3 |
2025-01-28 |
0.10.3* |
nvim |
nvim, text editor |
utilities |
|
|
| ripgrep |
aarch64 |
14.1.1 |
2025-01-29 |
14.1.1* |
rg |
rg, ripgrep |
utilities |
link |
|
| nvim |
aarch64 |
0.10.3 |
2025-01-29 |
0.10.3* |
nvim |
nvim, text editor |
utilities |
|
|
| vina |
x86_64 |
1.2.6 |
2025-02-04 |
1.2.6* |
vina, ... |
vina, autodock |
life sciences |
link |
|
| genblastg |
x86_64 |
1.39 |
2025-02-05 |
1.39* |
genblastG |
genBlast, identify groups of HSPs |
life sciences |
link |
link |
| R |
ppc64le |
4.4.2 |
2025-02-11 |
4.3.3, 4.4.2 |
R, ... |
R, jupyter |
languages |
link |
|
| jq |
ppc64le |
1.7.1 |
2025-02-12 |
1.7.1* |
jq |
jq, json |
utilities |
link |
|
| gw |
x86_64 |
1.1.4 |
2025-02-18 |
1.1.4* |
gw |
GW, fast browser for genomic sequencing data used directly from the terminal |
life sciences |
link |
link |
| R |
aarch64 |
4.4.2 |
2025-02-18 |
4.3.3, 4.4.2 |
R, ... |
R, jupyter |
languages |
link |
|
| fastplong |
x86_64 |
0.2.2 |
2025-02-19 |
0.2.2* |
fastplong |
fastplong, Ultra-fast preprocessing and quality control for long-read sequencing data |
life sciences |
link |
link |
| awscli |
x86_64 |
2.24.7 |
2025-02-19 |
2.24.7* |
aws, ... |
awscli, Universal Command Line Interface for Amazon Web Services |
life sciences |
link |
link |
| bcl2fastq2 |
x86_64 |
2.20.0.422 |
2025-02-19 |
2.20.0.422* |
bcl2fastq |
Bcl2Fastq, Demultiplex sequencing data and converts base call (BCL) files into FASTQ files |
life sciences |
link |
link |
| starship |
ppc64le |
1.22.1 |
2025-02-19 |
1.22.1* |
starship |
starship, prompt |
utilities |
|
|
| direnv |
ppc64le |
2.34.0 |
2025-02-20 |
2.34.0* |
direnv |
direnv, configuration |
utilities |
link |
|
| lsdeluxe |
ppc64le |
1.1.5 |
2025-02-20 |
1.1.5* |
lsd |
ls, lsd |
utilities |
link |
|
| lsdeluxe |
aarch64 |
1.1.5 |
2025-02-20 |
1.1.5* |
lsd |
ls, lsd |
utilities |
link |
|
| fd |
aarch64 |
10.2.0 |
2025-02-20 |
10.2.0* |
fd |
fd, find |
utilities |
link |
|
| fd |
ppc64le |
10.2.0 |
2025-02-20 |
10.2.0* |
fd |
fd, find |
utilities |
link |
|
| rattler-build |
ppc64le |
0.36.0 |
2025-02-21 |
0.36.0* |
rattler-build |
rattler-build, build |
utilities |
link, link |
|
| dos2unix |
ppc64le |
7.5.2 |
2025-02-22 |
7.5.2* |
dos2unix, ... |
dos2unix |
utilities |
link |
|
| blast |
ppc64le |
2.16.0 |
2025-02-23 |
2.16.0* |
blastn, ... |
blast, ncbi, alignment |
life sciences |
link |
link |
| blast |
aarch64 |
2.16.0 |
2025-02-23 |
2.16.0* |
blastn, ... |
blast, ncbi, alignment |
life sciences |
link |
link |
| bwa |
aarch64 |
0.7.18 |
2025-02-23 |
0.7.18* |
bwa, ... |
bwa, alignment, short-read, omics |
life sciences |
link |
link |
| bwa |
ppc64le |
0.7.18 |
2025-02-23 |
0.7.18* |
bwa, ... |
bwa, alignment, short-read, omics |
life sciences |
link |
link |
| salmon |
x86_64 |
1.10.3 |
2025-02-24 |
1.10.3* |
salmon |
Salmon, Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads |
life sciences |
link |
link |
| samtools |
aarch64 |
1.21 |
2025-02-25 |
1.21* |
samtools, ... |
samtools, bcftools, alignment |
life sciences |
link, link, link |
link |
| nodejs |
aarch64 |
22.11.0 |
2025-02-25 |
22.11.0 |
node, ... |
node, nodejs, npm |
languages |
link |
|
| nodejs |
ppc64le |
22.11.0 |
2025-02-25 |
22.11.0, 18.19.1 |
node, ... |
node, nodejs, npm |
languages |
link |
|
| samtools |
ppc64le |
1.21 |
2025-02-25 |
1.21* |
samtools, ... |
samtools, bcftools, alignment |
life sciences |
link, link, link |
link |
| bandage |
x86_64 |
0.8.1 |
2025-02-25 |
0.8.1* |
Bandage |
Bandage, Bioinformatics Application for Navigating De novo Assembly Graphs |
life sciences |
link |
link |
| mmseqs2 |
x86_64 |
17 |
2025-02-25 |
17* |
mmseqs |
mmseqs2, mmseqs, alignment, clustering, search |
life sciences |
link |
link |
| mmseqs2 |
ppc64le |
17 |
2025-02-25 |
17* |
mmseqs |
mmseqs2, mmseqs, alignment, clustering, search |
life sciences |
link |
link |
| mmseqs2 |
aarch64 |
17 |
2025-02-25 |
17* |
mmseqs |
mmseqs2, mmseqs, alignment, clustering, search |
life sciences |
link |
link |
| rattler-build |
aarch64 |
0.36.0 |
2025-02-26 |
0.36.0* |
rattler-build |
rattler-build, build |
utilities |
link, link |
|
| diamond |
aarch64 |
2.1.11 |
2025-02-26 |
2.1.11 |
diamond |
diamond, blast, alignment |
life sciences |
link, link |
link |
| diamond |
ppc64le |
2.1.11 |
2025-02-26 |
2.1.11 |
diamond |
diamond, blast, alignment |
life sciences |
link, link |
link |
| trim-galore |
x86_64 |
0.6.10 |
2025-03-06 |
0.6.10* |
trim_galore |
Trim Galore, wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files |
life sciences |
link |
link |
| biom-format |
x86_64 |
2.1.16 |
2025-03-20 |
2.1.16* |
biom |
biom, metabarcoding |
life sciences |
link |
link |
| direnv |
aarch64 |
2.34.0 |
2025-03-21 |
2.34.0* |
direnv |
direnv, configuration |
utilities |
link |
|
| prodigy-prot |
x86_64 |
2.2.5 |
2025-03-25 |
2.2.5* |
prodigy |
PRODIGY, Binding affinity predictor based on Intermolecular Contacts |
life sciences |
link |
link |
| haddock3 |
x86_64 |
2024.10.0b7 |
2025-03-25 |
2024.10.0b7* |
haddock3 |
HADDOCK, High Ambiguity Driven protein-protein DOCKing |
life sciences |
link |
link |
| gromacs |
x86_64 |
2024.5 |
2025-03-25 |
2024.5* |
gmx |
GROMACS, versatile package to perform molecular dynamics |
life sciences |
link |
link |
| dgenies |
x86_64 |
1.5.0 |
2025-03-31 |
1.5.0* |
dgenies |
D-GENIES, Dotplot large Genomes in an Interactive, Efficient and Simple way |
life sciences |
link |
link |
| wgatools |
x86_64 |
1.0.0 |
2025-03-31 |
1.0.0* |
wgatools |
wgatools, ultrafast toolkit for manipulating whole genome alignments |
life sciences |
link |
link |
| polypolish |
x86_64 |
0.6.0 |
2025-05-06 |
0.6.0* |
polypolish |
polypolish, long-reads, polishing, assembly |
life sciences |
link |
link |
| deeptools |
x86_64 |
3.5.6 |
2025-05-15 |
3.5.6* |
deeptools, ... |
deeptools, omics, deep sequencing |
life sciences |
link |
link |
| hifiasm |
x86_64 |
0.25.0 |
2025-05-20 |
0.25.0* |
hifiasm |
hifiasm, assembly, long-read, omics |
life sciences |
link |
link, link, link |
| falco |
x86_64 |
1.2.5 |
2025-05-27 |
1.2.5* |
falco |
falco, drop-in C++ implementation of FastQC |
life sciences |
link |
link |
| sequali |
x86_64 |
1.0.1 |
2025-05-27 |
1.0.1* |
sequali, ... |
Sequali, Fast sequencing data quality metrics |
life sciences |
link |
link |
| htslib |
x86_64 |
1.22.1 |
2025-05-27 |
1.21, 1.22.1* |
annot-tsv, ... |
HTSlib, C library for high-throughput sequencing data formats |
life sciences |
link |
link |
| intervene |
x86_64 |
0.6.5 |
2025-05-27 |
0.6.5* |
intervene |
Intervene, tool for intersection and visualization of multiple genomic region and gene sets |
life sciences |
link |
link |
| alignoth |
x86_64 |
0.16.0 |
2025-05-28 |
0.16.0* |
alignoth |
alignoth, tool for creating alignment plots from bam files |
life sciences |
link |
link |
| meeko |
x86_64 |
0.6.1 |
2025-06-04 |
0.6.1* |
mk_export.py, ... |
Meeko, Interface for AutoDock, molecule parameterization |
life sciences |
link |
link |
| autogrid |
x86_64 |
4.2.9 |
2025-06-04 |
4.2.9* |
autogrid4 |
AutoGrid, Calculates grids for AutoDock and AutoDock-GPU |
life sciences |
link |
link |
| idr |
x86_64 |
2.0.4.2 |
2025-06-17 |
2.0.4.2* |
idr |
IDR, Irreproducible Discovery Rate |
life sciences |
link |
link |
| btop |
aarch64 |
1.4.4 |
2025-07-04 |
1.4.4* |
btop |
btop, top |
utilities |
link |
|
| famsa |
x86_64 |
2.4.1 |
2025-07-21 |
2.4.1* |
famsa |
FAMSA2, ultra-scale multiple sequence alignments |
life sciences |
link |
link |
| verkko |
x86_64 |
2.2.1 |
2025-07-21 |
2.2.1* |
verkko |
Verkko, Telomere-to-telomere assembly of accurate long reads |
life sciences |
link |
link |
| hifiasm_meta |
x86_64 |
0.3.3 |
2025-07-22 |
0.3.3* |
hifiasm_meta |
hifiasm_meta, de novo metagenome assembler |
life sciences |
link |
link |
| readfq |
x86_64 |
2015.8.30 |
2025-07-28 |
2015.8.30* |
readfq |
readfq, simple tool to calculate reads number and total base count in FASTQ file |
life sciences |
link |
link |
| ssu-align |
x86_64 |
0.1.1 |
2025-07-30 |
0.1.1* |
ssu-align, ... |
SSU-ALIGN, identifying, aligning, masking and visualizing 16S and 18S SSU rRNA sequences |
life sciences |
link |
link |
| funannotate |
x86_64 |
1.8.17 |
2025-07-30 |
1.8.17* |
funannotate |
funannotate, eukaryotic genome annotation pipeline |
life sciences |
link |
link |
| circexplorer2 |
x86_64 |
2.3.8 |
2025-08-01 |
2.3.8* |
CIRCexplorer2 |
CIRCexplorer2, Circular RNA analysis toolkits |
life sciences |
link |
link |
| bwa-mem2 |
x86_64 |
2.3 |
2025-08-25 |
2.3* |
bwa-mem2 |
bwa-mem2, next version of bwa-mem |
life sciences |
link |
link |
| ncbi-datasets-cli |
x86_64 |
18.6.0 |
2025-08-28 |
18.6.0* |
datasets, ... |
datasets, gather data from across NCBI databases |
life sciences |
link |
link |
| pirate |
x86_64 |
1.0.5 |
2025-09-23 |
1.0.5* |
PIRATE, ... |
pirate, PIRATE, omics, orthology |
life sciences |
link, link |
link |
| xh |
x86_64 |
0.25.0 |
2025-09-24 |
0.25.0* |
xh, ... |
xh, curl, http client |
utilities |
link |
|
| racon |
x86_64 |
1.5.0 |
2025-09-29 |
1.5.0* |
racon, ... |
Racon, Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads |
life sciences |
link |
link |
| pyrodigal |
x86_64 |
3.6.3.post1 |
2025-09-29 |
3.6.3.post1* |
pyrodigal |
Pyrodigal, Python interface to Prodigal |
life sciences |
link |
link |
| aster |
x86_64 |
1.23 |
2025-10-13 |
1.23* |
astral, ... |
ASTER, Accurate Species Tree EstimatoR |
life sciences |
link |
link |