Alternatives and similar repositories for hisat2

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

• FelixKrueger / TrimGalore
  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…
  ☆536Updated last week
• bwa-mem2 / bwa-mem2
  The next version of bwa-mem
  ☆810Updated 3 months ago
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆440Updated 5 months ago
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆459Updated last year
• NBISweden / AGAT
  Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/
  ☆554Updated 2 weeks ago
• s-andrews / FastQC
  A quality control analysis tool for high throughput sequencing data
  ☆572Updated 3 weeks ago
• lindenb / jvarkit
  Java utilities for Bioinformatics
  ☆515Updated last month
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆480Updated last month
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆451Updated last year
• usadellab / Trimmomatic
  ☆284Updated 3 months ago
• mikolmogorov / Flye
  De novo assembler for single molecule sequencing reads using repeat graphs
  ☆893Updated 8 months ago
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆752Updated 6 months ago
• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆689Updated 7 months ago
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆505Updated 2 months ago
• aidenlab / juicer
  A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
  ☆474Updated 4 months ago
• fritzsedlazeck / Sniffles
  Structural variation caller using third generation sequencing
  ☆631Updated last month
• chhylp123 / hifiasm
  Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
  ☆721Updated 10 months ago
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆767Updated 2 months ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆558Updated last year
• Illumina / hap.py
  Haplotype VCF comparison tools
  ☆455Updated 2 years ago
• deeptools / pyGenomeTracks
  python module to plot beautiful and highly customizable genome browser tracks
  ☆862Updated last year
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆302Updated 2 years ago
• Illumina / strelka
  Strelka2 germline and somatic small variant caller
  ☆389Updated 4 years ago
• BenLangmead / bowtie2
  A fast and sensitive gapped read aligner
  ☆766Updated 2 months ago
• ablab / quast
  Genome assembly evaluation tool
  ☆488Updated last year
• nf-core / sarek
  Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
  ☆538Updated this week
• marbl / canu
  A single molecule sequence assembler for genomes large and small.
  ☆695Updated 2 months ago
• Illumina / manta
  Structural variant and indel caller for mapped sequencing data
  ☆458Updated 3 months ago
• davidemms / OrthoFinder
  Phylogenetic orthology inference for comparative genomics
  ☆827Updated 6 months ago
• mummer4 / mummer
  Mummer alignment tool
  ☆547Updated 11 months ago