Alternatives and similar repositories for samtools

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

• gt1 / biobambam
  Tools for bam file processing
  ☆55Updated 10 years ago
• Illumina / isaac2
  Aligner for sequencing data
  ☆21Updated 9 years ago
• arq5x / bedtools-protocols
  ☆78Updated 11 years ago
• cc2qe / vawk
  An awk-like VCF parser
  ☆56Updated 2 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 3 years ago
• ekg / bamaddrg
  adds sample names and read-group (RG) tags to BAM alignments
  ☆51Updated 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…
  ☆68Updated 11 years ago
• lh3 / bgt
  Flexible genotype query among 30,000+ samples whole-genome
  ☆94Updated 6 years ago
• kenchen / breakdancer
  SV detection from paired end reads mapping
  ☆38Updated 15 years ago
• lh3 / fermikit
  De novo assembly based variant calling pipeline for Illumina short reads
  ☆110Updated 5 years ago
• mattloose / RUscripts
  Scripts for implementing read until and other examples.
  ☆31Updated 5 years ago
• Cibiv / Teaser
  A tool to benchmark mappers and different parameters within minutes
  ☆44Updated 6 years ago
• lh3 / bfc
  High-performance error correction for Illumina resequencing data
  ☆74Updated 9 years ago
• aquaskyline / LRSIM
  10x Genomics Reads Simulator
  ☆46Updated 2 years ago
• bioinform / varsim
  VarSim: A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications
  ☆90Updated last year
• brentp / duphold
  don't get DUP'ed or DEL'ed by your putative SVs.
  ☆107Updated 5 years ago
• relipmoc / skewer
  ☆96Updated 3 years ago
• EarlhamInst / NanoOK
  Analysis tool for Nanopore sequencing data
  ☆34Updated 6 years ago
• ssadedin / bazam
  A read extraction and realignment tool for next generation sequencing data
  ☆104Updated 3 years ago
• mozack / abra
  Assembly Based ReAligner
  ☆74Updated 7 years ago
• lh3 / fermi-lite
  Standalone C library for assembling Illumina short reads in small regions
  ☆72Updated 3 years ago
• riverlee / MitoSeek
  Seeking information like heteroplasmy, structure variants, etc. on Mitochondrial genome from next generation sequencing
  ☆41Updated 7 years ago
• jgurtowski / nanocorr
  Error correction for Oxford Nanopore data
  ☆47Updated 4 years ago
• dzerbino / oases
  De novo transcriptome assembler for short reads
  ☆64Updated 7 years ago
• lh3 / sgdp-fermi
  FermiKit small variant calls for public SGDP samples
  ☆17Updated 9 years ago
• mcfrith / last-rna
  ☆49Updated 3 years ago
• svviz / svviz
  Read visualizer for structural variants
  ☆84Updated 7 years ago
• i5K-KINBRE-script-share / Irys-scaffolding
  scripts to parse IrysView output
  ☆39Updated 10 years ago
• walaj / bxtools
  Tools for analyzing 10X Genomics data
  ☆42Updated 6 years ago
• gogetdata / ggd-recipes
  conda recipes for genomic data
  ☆84Updated 4 years ago