Alternatives and similar repositories for samtools

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

• lh3 / bfc
  High-performance error correction for Illumina resequencing data
  ☆73Updated 9 years ago
• arq5x / bedtools-protocols
  ☆78Updated 11 years ago
• cc2qe / vawk
  An awk-like VCF parser
  ☆56Updated last year
• gt1 / biobambam
  Tools for bam file processing
  ☆55Updated 10 years ago
• benedictpaten / marginAlign
  UCSC Nanopore
  ☆43Updated 6 years ago
• Illumina / isaac2
  Aligner for sequencing data
  ☆21Updated 9 years ago
• Cibiv / Teaser
  A tool to benchmark mappers and different parameters within minutes
  ☆44Updated 6 years ago
• ekg / bamaddrg
  adds sample names and read-group (RG) tags to BAM alignments
  ☆51Updated 4 years ago
• relipmoc / skewer
  ☆95Updated 3 years ago
• kenchen / breakdancer
  SV detection from paired end reads mapping
  ☆38Updated 15 years ago
• Cibiv / NextGenMap
  NextGenMap is a flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms whil…
  ☆88Updated 6 years ago
• mattloose / RUscripts
  Scripts for implementing read until and other examples.
  ☆32Updated 5 years ago
• jstjohn / SimSeq
  An illumina paired-end and mate-pair short read simulator. This project attempts to model as many of the quirks that exist in Illumina da…
  ☆67Updated 11 years ago
• lh3 / fermikit
  De novo assembly based variant calling pipeline for Illumina short reads
  ☆108Updated 4 years ago
• walaj / bxtools
  Tools for analyzing 10X Genomics data
  ☆42Updated 6 years ago
• mcfrith / last-rna
  ☆49Updated 2 years ago
• jgurtowski / nanocorr
  Error correction for Oxford Nanopore data
  ☆47Updated 4 years ago
• deaconjs / ThousandVariantCallersRepo
  Thousand Variant Callers Project Repository
  ☆73Updated 6 years ago
• lh3 / bgt
  Flexible genotype query among 30,000+ samples whole-genome
  ☆94Updated 6 years ago
• RealTimeGenomics / rtg-core
  RTG Core: Software for alignment and analysis of next-gen sequencing data.
  ☆48Updated 4 months ago
• mozack / abra
  Assembly Based ReAligner
  ☆74Updated 7 years ago
• lh3 / CHM-eval
  ☆54Updated 5 years ago
• ssadedin / bazam
  A read extraction and realignment tool for next generation sequencing data
  ☆103Updated 2 years ago
• jts / nanocorrect
  Experimental pipeline for correcting nanopore reads
  ☆39Updated 8 years ago
• Oshlack / STRetch
  Method for detecting STR expansions from short-read sequencing data
  ☆63Updated 3 years ago
• aquaskyline / LRSIM
  10x Genomics Reads Simulator
  ☆45Updated last year
• brentp / duphold
  don't get DUP'ed or DEL'ed by your putative SVs.
  ☆106Updated 4 years ago
• tk2 / RetroSeq
  RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference…
  ☆67Updated 2 years ago
• lh3 / tabtk
  Toolkit for processing TAB-delimited format
  ☆62Updated last year
• peterjc / picobio
  Miscellaneous Bioinformatics scripts etc mostly in Python
  ☆45Updated last week