Alternatives and similar repositories for bowtie

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

• pezmaster31 / bamtools
  C++ API & command-line toolkit for working with BAM data
  ☆429Updated 3 months ago
• bcgsc / abyss
  Assemble large genomes using short reads
  ☆322Updated 5 months ago
• lh3 / wgsim
  Reads simulator
  ☆282Updated 3 years ago
• cole-trapnell-lab / cufflinks
  ☆317Updated 5 years ago
• dzerbino / velvet
  Short read de novo assembler using de Bruijn graphs, as published in: D.R. Zerbino and E. Birney. 2008. Velvet: algorithms for de novo sh…
  ☆293Updated 7 years ago
• bedops / bedops
  BEDOPS: high-performance genomic feature operations
  ☆351Updated 4 months ago
• jts / sga
  de novo sequence assembler using string graphs
  ☆241Updated 6 years ago
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆486Updated 2 weeks ago
• arq5x / lumpy-sv
  lumpy: a general probabilistic framework for structural variant discovery
  ☆333Updated 3 years ago
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆318Updated 3 years ago
• isovic / graphmap
  GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/n…
  ☆182Updated 6 years ago
• gmarcais / Jellyfish
  A fast multi-threaded k-mer counter
  ☆509Updated last year
• brentp / vcfanno
  annotate a VCF with other VCFs/BEDs/tabixed files
  ☆383Updated last month
• DaehwanKimLab / tophat
  Spliced read mapper for RNA-Seq
  ☆92Updated 2 years ago
• Illumina / strelka
  Strelka2 germline and somatic small variant caller
  ☆377Updated 3 years ago
• nanopore-wgs-consortium / NA12878
  Data and analysis for NA12878 genome on nanopore
  ☆397Updated 2 years ago
• ENCODE-DCC / kentUtils
  UCSC command line bioinformatic utilities
  ☆184Updated last year
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆459Updated last week
• marbl / MashMap
  A fast approximate aligner for long DNA sequences
  ☆282Updated 10 months ago
• hall-lab / speedseq
  A flexible framework for rapid genome analysis and interpretation
  ☆317Updated 2 years ago
• RealTimeGenomics / rtg-tools
  RTG Tools: Utilities for accurate VCF comparison and manipulation
  ☆323Updated 3 months ago
• genome-in-a-bottle / giab_data_indexes
  This repository contains data indexes from NIST's Genome in a Bottle project.
  ☆254Updated last year
• OpenGene / AfterQC
  Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
  ☆211Updated 5 years ago
• genome / pindel
  Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants …
  ☆174Updated 5 years ago
• genometools / genometools
  GenomeTools genome analysis system.
  ☆321Updated last year
• Illumina / hap.py
  Haplotype VCF comparison tools
  ☆441Updated last year
• luntergroup / octopus
  Bayesian haplotype-based mutation calling
  ☆318Updated last month
• marbl / Mash
  Fast genome and metagenome distance estimation using MinHash
  ☆418Updated last year
• rrwick / Bandage
  a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
  ☆631Updated 2 years ago
• freebayes / freebayes
  Bayesian haplotype-based genetic polymorphism discovery and genotyping.
  ☆840Updated 3 months ago