This category comprises a large proportion of the apps installed on the NIH HPC systems. It includes "pipelines" that allow data to flow through several stages of analysis and Next Generation Sequencing (NGS) applications.
- ATAC-Seq / DNase-Seq Pipeline
- AscatNGS
- Atropos
- BAMSurgeon
- BRASS
- Canvas
- MAGGIE
- PCAP-core
- PePr
- RSD
- SURPI
- TPMCalculator
- TVC
- VAGrENT
- VEP
- abruijn
- bamliquidator
- bamreadcount
- bamutil
- bigscale2
- biom-format
- bison
- busco
- cancerit-wgs
- cellsnp
- cgpBattenberg
- cicero
- cnvkit
- cnvnator
- crispresso
- crossmap
- csvkit
- cutadapt
- deepsignal
- deeptools
- deepvariant
- delly
- dropest
- eager
- epic2
- flappie
- flye
- freebayes
- fusioninspector
- gossamer
- gridss
- guppy
- hail
- hap.py
- hicexplorer
- hicpro
- htseq
- humann2
- idep
- lefse
- macs
- mageck-vispr
- medaka
- megalodon
- metabat
- metaphlan
- mitosuite
- mtoolbox
- multiqc
- neusomatic
- parliament
- pvactools
- pychopper
- raremetal
- repeatmodeler
- ricopili
- rilseq
- rmats
- rnapeg
- rseqc
- salmon
- scramble
- seqlinkage
- sicer
- slamdunk
- stream
- sve
- svtk
- svtyper
- taiji
- tandemtools
- tetoolkit
- transvar
- umitools
- vireosnp
- xengsort