Alternatives and similar repositories for ngs

Users that are interested in ngs are comparing it to the libraries listed below

• gt1 / biobambam2
  Tools for early stage alignment file processing
  ☆95Updated 6 years ago
• ewels / clusterflow
  A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.
  ☆98Updated 2 years ago
• dnanexus-rnd / GLnexus
  Scalable gVCF merging and joint variant calling for population sequencing projects
  ☆174Updated last year
• ncbi / ncbi-vdb
  ncbi-vdb
  ☆93Updated this week
• andyrimmer / Platypus
  Platypus Variant Caller
  ☆108Updated last year
• bioinform / varsim
  VarSim: A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications
  ☆90Updated last year
• dcjones / fastq-tools
  Small utilities for working with fastq sequence files.
  ☆123Updated 3 years ago
• ncbi / sratoolkit
  SRAToolkit has been REPLACED - see README
  ☆38Updated 9 years ago
• ewels / AWS-iGenomes
  Documentation and description of AWS iGenomes S3 resource.
  ☆120Updated last year
• lh3 / fermikit
  De novo assembly based variant calling pipeline for Illumina short reads
  ☆110Updated 5 years ago
• kingsfordgroup / sailfish
  Rapid Mapping-based Isoform Quantification from RNA-Seq Reads
  ☆127Updated 3 years ago
• CGATOxford / cgat
  Do not use - please refer to our newest code: https://github.com/cgat-developers/cgat-apps
  ☆124Updated 7 years ago
• hall-lab / svtools
  Tools for processing and analyzing structural variants.
  ☆156Updated 3 years ago
• atks / vt
  A tool set for short variant discovery in genetic sequence data.
  ☆204Updated 4 years ago
• ngsutils / ngsutils
  Tools for next-generation sequencing analysis
  ☆89Updated 6 years ago
• CCDG / Pipeline-Standardization
  ☆81Updated 7 years ago
• fls-bioinformatics-core / genomics
  Scripts, utilities and programs for genomic bioinformatics.
  ☆83Updated 2 months ago
• ncbi / ngs-tools
  ☆108Updated 2 months ago
• statgen / bamUtil
  ☆92Updated 4 years ago
• alyssafrazee / ballgown
  Bioconductor package "ballgown", devel version. Isoform-level differential expression analysis in R.
  ☆148Updated 4 years ago
• brentp / bio-playground
  miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.
  ☆182Updated 7 years ago
• bioconda / bioconda-utils
  Utilities for building and managing bioconda recipes
  ☆103Updated last month
• jstjohn / SeqPrep
  Tool for stripping adaptors and/or merging paired reads with overlap into single reads.
  ☆145Updated 9 years ago
• Illumina / interop
  C++ Library to parse Illumina InterOp files
  ☆80Updated last month
• mdshw5 / fastqp
  Simple FASTQ quality assessment using Python
  ☆109Updated 4 years ago
• DaehwanKimLab / tophat
  Spliced read mapper for RNA-Seq
  ☆92Updated 2 years ago
• KHP-Informatics / ngseasy
  Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)
  ☆86Updated 8 years ago
• relipmoc / skewer
  ☆96Updated 3 years ago
• nygenome / lancet
  Microassembly based somatic variant caller for NGS data
  ☆154Updated 3 years ago
• alastair-droop / fqtools
  An efficient FASTQ manipulation suite
  ☆138Updated 6 years ago