RCAC Biocontainers documentation!
This is the user guide for biocontainer modules deployed in Purdue High Performance Computing clusters. More information about our center is avaiable here (https://www.rcac.purdue.edu).
If you have any question, contact me(Yucheng Zhang) at: zhan4429@purdue.edu
Warning
Do not use both bioinfo and biocontainers in your job script, because loading bioinfo will cause the failure of loading many modules including biocontainers in Brown, Halstead, Scholar, Workbench, and Gilbreth. Since RCAC will not provide support to bioinfo in the future clusters, we recommend users to just use biocontainers.
Frequently Asked Questions
Singularity
Application list
- 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
- Ariba
- Ascatngs
- 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
- BEAST 2
- Bedops
- Bedtools
- Bioawk
- Biobambam
- Bioconvert
- Biopython
- Bismark
- Blasr
- BLAST
- BlobTools
- Bmge
- Bowtie
- Bowtie 2
- Bracken
- BRAKER
- 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
- 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
- Covgen
- Cramino
- CRISPRCasFinder
- Crispresso2
- Crispritz
- Crossmap
- cross_match
- Csvkit
- Csvtk
- Cufflinks
- Cutadapt
- Cuttlefish
- Cyvcf2
- Das_tool
- Dbg2olc
- Debreak
- Deconseq
- Deepbgc
- Deepconsensus
- Deepsignal2
- DeepTools
- Deepvariant
- Delly
- Dendropy
- Diamond
- Dnaapler
- 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
- Fq
- Fraggenescan
- Fraggenescanrs
- Freebayes
- Freyja
- Fseq
- Ftp
- Funannotate
- Fwdpy11
- Gadma
- Gambit
- Gamma
- Gangstr
- Gapfiller
- Gapit
- GATK
- GATK4
- Gemma
- Gemoma
- GeneMark-ES/ET/EP
- 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
- GTDB-Tk
- Gubbins
- Guppy
- Hail
- Hap.py
- Helen
- Hicexplorer
- Hic-pro
- Hifiasm
- HISAT2
- Hmmer
- HOMMER
- Homopolish
- How_are_we_stranded_here
- HTSeq
- Htslib
- Htstream
- HUMAnN 3
- Hyphy
- Hypo
- Idba
- IGV
- Impute2
- Infernal
- Instrain
- Intarna
- InterProScan
- IQ-TREE
- Iqtree2
- Ismapper
- Isoquant
- Isoseq3
- Ivar
- Jcvi
- Kaiju
- Kakscalculator2
- Kallisto
- Kentutils
- Khmer
- Kissde
- Kissplice
- Kissplice2refgenome
- Kma
- Kmc
- Kmergenie
- 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
- Mapdamage2
- Marginpolish
- Mash
- Mashmap
- Mashtree
- Masurca
- Mauve
- Maxbin2
- Maxquant
- Mcl
- Mcscanx
- Medaka
- Megadepth
- Megahit
- Megan
- Meme
- Memes
- Meraculous
- Merqury
- Meryl
- Metabat
- Metachip
- MetaPhlAn 3
- 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
- Nextdenovo
- Nextflow
- Nextpolish
- Ngs-bits
- Ngsld
- Ngsutils
- Odgi
- OrthoFinder
- Paml
- Panacota
- Panaroo
- Pandaseq
- Pandora
- Pangolin
- Pangraph
- PanPhlAn
- Clara Parabricks
- Parallel-fastq-dump
- Parliament2
- Parsnp
- Pasapipeline
- Pasta
- Pblat
- Pbmm2
- Pbptyper
- PCAngsd
- Peakranger
- Pepper_deepvariant
- BioPerl
- Pggb
- Phast
- Phd2fasta
- Phg
- Phipack
- phrap
- phred
- Phylofisher
- Phylosuite
- Picard Tools
- 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
- QIIME 2
- Qtlseq
- Qualimap
- Quast
- QuickMIRSeq
- R
- Racon
- Ragout
- Ragtag
- Rapmap
- Rasusa
- Raven-assembler
- Raxml
- Raxml-ng
- R-cellchat
- Reapr
- Rebaler
- Reciprocal Smallest Distance
- Recycler
- Regtools
- RepeatMasker
- RepeatModeler
- RepeatScout
- Resfinder
- Revbayes
- rMATS
- rmats2sashimiplot
- RNAIndel
- RNApeg
- Rnaquast
- Roary
- r-rnaseq
- 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
- SignalP
- 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-Toolkit
- Srst2
- Stacks
- STAR
- Staramr
- STAR-Fusion
- 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 Executables
- Umi_tools
- 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
- Wtdbg2