Alternatives and similar repositories for samtools

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

• arq5x / bedtools-protocols
  ☆78Updated 11 years ago
• gt1 / biobambam
  Tools for bam file processing
  ☆55Updated 10 years ago
• lh3 / bfc
  High-performance error correction for Illumina resequencing data
  ☆73Updated 9 years ago
• ekg / bamaddrg
  adds sample names and read-group (RG) tags to BAM alignments
  ☆51Updated 4 years ago
• Cibiv / Teaser
  A tool to benchmark mappers and different parameters within minutes
  ☆44Updated 6 years ago
• cc2qe / vawk
  An awk-like VCF parser
  ☆56Updated last year
• Illumina / isaac2
  Aligner for sequencing data
  ☆21Updated 9 years ago
• sequencing / NxTrim
  Adapter trimming and virtual library creation for Illumina Nextera Mate Pair libraries.
  ☆53Updated 7 years ago
• ssadedin / bazam
  A read extraction and realignment tool for next generation sequencing data
  ☆103Updated 3 years ago
• guyduche / Blast2Bam
  Blast2Bam uses the XML results of Blastn, the reference and the fastQ or fasta file(s) to output a SAM file.
  ☆50Updated 4 years ago
• aquaskyline / LRSIM
  10x Genomics Reads Simulator
  ☆46Updated last year
• i5K-KINBRE-script-share / Irys-scaffolding
  scripts to parse IrysView output
  ☆39Updated 10 years ago
• enasequence / cramtools
  CRAM format specification and java API for read data.
  ☆59Updated 7 years ago
• jgurtowski / nanocorr
  Error correction for Oxford Nanopore data
  ☆47Updated 4 years ago
• EarlhamInst / NanoOK
  Analysis tool for Nanopore sequencing data
  ☆34Updated 6 years ago
• lh3 / bgt
  Flexible genotype query among 30,000+ samples whole-genome
  ☆94Updated 6 years ago
• peterjc / picobio
  Miscellaneous Bioinformatics scripts etc mostly in Python
  ☆45Updated 3 weeks ago
• mcfrith / last-rna
  ☆49Updated 2 years ago
• ljdursi / mergevcf
  Python package and routines for merging VCF files
  ☆29Updated 4 years ago
• deaconjs / ThousandVariantCallersRepo
  Thousand Variant Callers Project Repository
  ☆74Updated 6 years ago
• RealTimeGenomics / rtg-core
  RTG Core: Software for alignment and analysis of next-gen sequencing data.
  ☆48Updated 6 months 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
• COMBINE-lab / RapMap
  Rapid sensitive and accurate read mapping via quasi-mapping
  ☆90Updated 5 years ago
• ekg / fastahack
  utilities for indexing and sequence extraction from FASTA files
  ☆59Updated 4 years ago
• relipmoc / skewer
  ☆96Updated 3 years ago
• Oshlack / Lace
  Building SuperTranscripts: A linear representation of transcriptome data
  ☆68Updated 4 years ago
• walaj / bxtools
  Tools for analyzing 10X Genomics data
  ☆42Updated 6 years ago
• brwnj / covviz
  Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata
  ☆58Updated 3 years ago
• mattloose / RUscripts
  Scripts for implementing read until and other examples.
  ☆31Updated 5 years ago
• lh3 / fermikit
  De novo assembly based variant calling pipeline for Illumina short reads
  ☆110Updated 4 years ago