Alternatives and similar repositories for samtools

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

• aquaskyline / LRSIM
  10x Genomics Reads Simulator
  ☆45Updated last year
• cc2qe / vawk
  An awk-like VCF parser
  ☆56Updated last year
• arq5x / bedtools-protocols
  ☆78Updated 11 years ago
• gt1 / biobambam
  Tools for bam file processing
  ☆55Updated 10 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
• Cibiv / Teaser
  A tool to benchmark mappers and different parameters within minutes
  ☆44Updated 6 years ago
• sequencing / gvcftools
  Utilities to create and analyze gVCF files
  ☆38Updated 8 years ago
• lh3 / CHM-eval
  ☆54Updated 5 years ago
• lh3 / bfc
  High-performance error correction for Illumina resequencing data
  ☆73Updated 9 years ago
• lh3 / bgt
  Flexible genotype query among 30,000+ samples whole-genome
  ☆94Updated 6 years ago
• ekg / bamaddrg
  adds sample names and read-group (RG) tags to BAM alignments
  ☆51Updated 4 years ago
• schatzlab / appliedgenomics2017
  JHU EN.600.649: Computational Genomics: Applied Comparative Genomics
  ☆58Updated 7 years ago
• lh3 / fermikit
  De novo assembly based variant calling pipeline for Illumina short reads
  ☆108Updated 4 years ago
• svviz / svviz
  Read visualizer for structural variants
  ☆84Updated 7 years ago
• walaj / bxtools
  Tools for analyzing 10X Genomics data
  ☆42Updated 6 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
• brentp / duphold
  don't get DUP'ed or DEL'ed by your putative SVs.
  ☆106Updated 4 years ago
• benedictpaten / marginAlign
  UCSC Nanopore
  ☆43Updated 6 years ago
• mklarqvist / tomahawk
  Fast calculations of linkage-disequilibrium in large-scale human cohorts
  ☆44Updated 5 years ago
• ryanlayer / gqt
  A genotype query interface.
  ☆136Updated 4 years ago
• 10XGenomics / lariat
  Linked-Read Alignment Tool
  ☆26Updated 6 years ago
• arq5x / grabix
  a wee tool for random access into BGZF files.
  ☆85Updated 7 years ago
• TGAC / NanoOK
  Analysis tool for Nanopore sequencing data
  ☆34Updated 6 years ago
• Oshlack / Lace
  Building SuperTranscripts: A linear representation of transcriptome data
  ☆67Updated 4 years ago
• bioinform / metasv
  MetaSV: An accurate and integrative structural-variant caller for next generation sequencing
  ☆58Updated 8 years ago
• mcfrith / last-rna
  ☆49Updated 2 years ago
• dzerbino / oases
  De novo transcriptome assembler for short reads
  ☆63Updated 7 years ago
• kenchen / breakdancer
  SV detection from paired end reads mapping
  ☆38Updated 15 years ago
• bioinform / varsim
  VarSim: A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications
  ☆89Updated 11 months ago
• Illumina / isaac2
  Aligner for sequencing data
  ☆21Updated 9 years ago