Biocontainers
Link to section 'What is BioContainers' of 'Biocontainers' What is BioContainers
The BioContainers project came from the idea of using the containers-based technologies such as Docker or rkt for bioinformatics software. Having a common and controllable environment for running software could help to deal with some of the current problems during software development and distribution. BioContainers is a community-driven project that provides the infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics fields such as proteomics, genomics, transcriptomics and metabolomics. . For more information, please visit BioContainers project.
Link to section 'Deployed Applications' of 'Biocontainers' Deployed Applications
- abacas
- abismal
- abpoa
- abricate
- abyss
- actc
- adapterremoval
- advntr
- afplot
- afterqc
- agat
- agfusion
- alfred
- alien-hunter
- alignstats
- allpathslg
- alphafold
- amptk
- ananse
- anchorwave
- angsd
- annogesic
- annovar
- antismash
- anvio
- any2fasta
- arcs
- asgal
- aspera-connect
- assembly-stats
- atac-seq-pipeline
- ataqv
- atram
- atropos
- augur
- augustus
- bactopia
- bali-phy
- bamgineer
- bamliquidator
- bam-readcount
- bamsurgeon
- bamtools
- bamutil
- barrnap
- basenji
- bayescan
- bazam
- bbmap
- bbtools
- bcftools
- bcl2fastq
- beagle
- beast2
- bedops
- bedtools
- bioawk
- biobambam
- bioconvert
- biopython
- bismark
- blasr
- blast
- blobtools
- bmge
- bowtie
- bowtie2
- bracken
- braker2
- brass
- breseq
- busco
- bustools
- bwa
- bwameth
- cactus
- cafe
- canu
- ccs
- cdbtools
- cd-hit
- cegma
- cellbender
- cellphonedb
- cellranger
- cellranger-arc
- cellranger-atac
- cellranger-dna
- cellrank
- cellrank-krylov
- cellsnp-lite
- celltypist
- centrifuge
- cfsan-snp-pipeline
- checkm-genome
- chewbbaca
- chopper
- chromap
- cicero
- circexplorer2
- circlator
- circompara2
- circos
- ciri2
- ciriquant
- clair3
- clairvoyante
- clearcnv
- clever-toolkit
- clonalframeml
- clust
- clustalw
- cnvkit
- cnvnator
- coinfinder
- concoct
- control-freec
- cooler
- coverm
- cramino
- crisprcasfinder
- crispresso2
- crispritz
- crossmap
- cross_match
- csvtk
- cufflinks
- cutadapt
- cuttlefish
- cyvcf2
- das_tool
- dbg2olc
- deconseq
- deepbgc
- deepconsensus
- deepsignal2
- deeptools
- deepvariant
- delly
- dendropy
- diamond
- dnaio
- dragonflye
- drep
- dropest
- drop-seq
- dsuite
- easysfs
- edta
- eggnog-mapper
- emboss
- ensembl-vep
- epic2
- evidencemodeler
- exonerate
- expansionhunter
- fasta3
- fastani
- fastp
- fastqc
- fastq_pair
- fastq-scan
- fastspar
- faststructure
- fasttree
- fastx_toolkit
- filtlong
- flye
- fraggenescan
- fraggenescanrs
- freebayes
- freyja
- fseq
- funannotate
- fwdpy11
- gadma
- gambit
- gamma
- gangstr
- gapfiller
- gatk
- gatk4
- gemma
- gemoma
- genemark
- genemarks-2
- genmap
- genomedata
- genomepy
- genomescope2
- genomicconsensus
- genrich
- getorganelle
- gfaffix
- gfastats
- gfatools
- gffcompare
- gffread
- gffutils
- gimmemotifs
- glimmer
- glimmerhmm
- glnexus
- gmap
- goatools
- graphlan
- graphmap
- gridss
- gseapy
- gtdbtk
- gubbins
- guppy
- hail
- hap.py
- helen
- hicexplorer
- hic-pro
- hifiasm
- hisat2
- hmmer
- homer
- how_are_we_stranded_here
- htseq
- htslib
- htstream
- humann
- hyphy
- idba
- igv
- impute2
- infernal
- instrain
- intarna
- interproscan
- iqtree
- isoquant
- isoseq3
- ivar
- jcvi
- kaiju
- kakscalculator2
- kallisto
- khmer
- kissde
- kissplice
- kissplice2refgenome
- kma
- kmc
- kmergenie
- kmer-jellyfish
- kneaddata
- kover
- kraken2
- krakentools
- lambda
- last
- lastz
- ldhat
- ldjump
- ldsc
- liftoff
- liftofftools
- lima
- links
- lofreq
- longphase
- longqc
- lra
- ltr_finder
- ltrpred
- lumpy-sv
- lyveset
- macrel
- macs2
- macs3
- mafft
- mageck
- magicblast
- maker
- manta
- mapcaller
- marginpolish
- mash
- mashmap
- mashtree
- masurca
- mauve
- maxbin2
- maxquant
- mcl
- mcscanx
- medaka
- megadepth
- megahit
- megan
- meme
- memes
- meraculous
- merqury
- meryl
- metabat
- metachip
- metaphlan
- metaseq
- methyldackel
- metilene
- mhm2
- microbedmm
- minialign
- miniasm
- minimap2
- minipolish
- miniprot
- mirdeep2
- mirtop
- mitofinder
- mlst
- mmseqs2
- mob_suite
- modbam2bed
- modeltest-ng
- momi
- mothur
- motus
- mrbayes
- multiqc
- mummer4
- muscle
- mutmap
- mykrobe
- n50
- nanofilt
- nanolyse
- nanoplot
- nanopolish
- ncbi-amrfinderplus
- ncbi-datasets
- ncbi-genome-download
- ncbi-table2asn
- neusomatic
- nextalign
- nextclade
- nextflow
- ngs-bits
- ngsld
- ngsutils
- orthofinder
- paml
- panacota
- panaroo
- pandaseq
- pandora
- pangolin
- panphlan
- parallel-fastq-dump
- parliament2
- parsnp
- pasta
- pbmm2
- pbptyper
- pcangsd
- peakranger
- pepper_deepvariant
- perl-bioperl
- phast
- phd2fasta
- phg
- phipack
- phrap
- phred
- phylosuite
- picard
- picrust2
- pilon
- pindel
- pirate
- piscem
- pixy
- plasmidfinder
- platon
- platypus
- plink
- plink2
- plotsr
- pomoxis
- poppunk
- popscle
- pplacer
- prinseq
- prodigal
- prokka
- proteinortho
- prothint
- pullseq
- purge_dups
- pvactools
- pyani
- pybedtools
- pybigwig
- pychopper
- pycoqc
- pyensembl
- pyfaidx
- pygenometracks
- pygenomeviz
- pyranges
- pysam
- pyvcf3
- qiime2
- qtlseq
- qualimap
- quast
- quickmirseq
- r
- racon
- ragout
- ragtag
- rapmap
- rasusa
- raven-assembler
- raxml
- raxml-ng
- reapr
- rebaler
- reciprocal_smallest_distance
- recycler
- regtools
- repeatmasker
- repeatmodeler
- repeatscout
- resfinder
- revbayes
- rmats
- rmats2sashimiplot
- rnaindel
- rnapeg
- rnaquast
- roary
- r-rnaseq
- r-rstudio
- r-scrnaseq
- rsem
- rseqc
- run_dbcan
- rush
- sage
- salmon
- sambamba
- samblaster
- samclip
- samplot
- samtools
- scanpy
- scarches
- scgen
- scirpy
- scvelo
- scvi-tools
- segalign
- seidr
- sepp
- seqcode
- seqkit
- seqyclean
- shapeit4
- shapeit5
- shasta
- shigeifinder
- shorah
- shortstack
- shovill
- sicer
- sicer2
- signalp4
- signalp6
- simug
- singlem
- ska
- skewer
- slamdunk
- smoove
- snakemake
- snap
- snap-aligner
- snaptools
- snippy
- snp-dists
- snpeff
- snpgenie
- snphylo
- snpsift
- snp-sites
- soapdenovo2
- sortmerna
- souporcell
- sourmash
- spaceranger
- spades
- sprod
- squeezemeta
- squid
- sra-tools
- srst2
- stacks
- star
- staramr
- starfusion
- stream
- stringdecomposer
- stringtie
- strique
- structure
- subread
- survivor
- svaba
- svtools
- svtyper
- swat
- syri
- talon
- targetp
- tassel
- taxonkit
- t-coffee
- tetranscripts
- tiara
- tigmint
- tobias
- tombo
- tophat
- tpmcalculator
- transabyss
- transdecoder
- transrate
- transvar
- trax
- treetime
- trimal
- trim-galore
- trimmomatic
- trinity
- trinotate
- trnascan-se
- trtools
- trust4
- trycycler
- ucsc_genome_toolkit
- unicycler
- usefulaf
- vadr
- vardict-java
- varlociraptor
- varscan
- vartrix
- vatools
- vcf2maf
- vcf2phylip
- vcf2tsvpy
- vcf-kit
- vcftools
- velocyto.py
- velvet
- veryfasttree
- vg
- viennarna
- vsearch
- weblogo
- whatshap
- wiggletools
- winnowmap
- wtdbg