Alternatives and similar repositories for hisat2

Users that are interested in hisat2 are comparing it to the libraries listed below

• bwa-mem2 / bwa-mem2
  The next version of bwa-mem
  ☆788Updated last week
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆741Updated 3 months ago
• FelixKrueger / TrimGalore
  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…
  ☆527Updated last month
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆470Updated this week
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆454Updated last year
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆434Updated 2 months ago
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆488Updated 2 months ago
• mikolmogorov / Flye
  De novo assembler for single molecule sequencing reads using repeat graphs
  ☆878Updated 5 months ago
• fritzsedlazeck / Sniffles
  Structural variation caller using third generation sequencing
  ☆622Updated this week
• s-andrews / FastQC
  A quality control analysis tool for high throughput sequencing data
  ☆544Updated 3 weeks ago
• NBISweden / AGAT
  Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/
  ☆535Updated last month
• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆664Updated 4 months ago
• usadellab / Trimmomatic
  ☆271Updated last week
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆441Updated 10 months ago
• aidenlab / juicer
  A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
  ☆463Updated last month
• freebayes / freebayes
  Bayesian haplotype-based genetic polymorphism discovery and genotyping.
  ☆845Updated 4 months ago
• DerrickWood / kraken2
  The second version of the Kraken taxonomic sequence classification system
  ☆837Updated last week
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆756Updated last week
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆555Updated last year
• davidemms / OrthoFinder
  Phylogenetic orthology inference for comparative genomics
  ☆803Updated 3 months ago
• BenLangmead / bowtie2
  A fast and sensitive gapped read aligner
  ☆747Updated last month
• chhylp123 / hifiasm
  Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
  ☆686Updated 7 months ago
• Illumina / strelka
  Strelka2 germline and somatic small variant caller
  ☆384Updated 3 years ago
• wdecoster / NanoPlot
  Plotting scripts for long read sequencing data
  ☆505Updated last month
• nservant / HiC-Pro
  HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
  ☆424Updated last year
• CGATOxford / UMI-tools
  Tools for handling Unique Molecular Identifiers in NGS data sets
  ☆526Updated 3 months ago
• lindenb / jvarkit
  Java utilities for Bioinformatics
  ☆511Updated last week
• trinityrnaseq / trinityrnaseq
  Trinity RNA-Seq de novo transcriptome assembly
  ☆875Updated 8 months ago
• mummer4 / mummer
  Mummer alignment tool
  ☆529Updated 8 months ago
• marbl / canu
  A single molecule sequence assembler for genomes large and small.
  ☆694Updated last month