Alternatives and similar repositories for hisat2:

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

• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆419Updated 3 weeks ago
• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆596Updated 10 months ago
• usadellab / Trimmomatic
  ☆235Updated 9 months ago
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆703Updated last week
• bwa-mem2 / bwa-mem2
  The next version of bwa-mem
  ☆741Updated 7 months ago
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆430Updated last year
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆725Updated 3 weeks ago
• FelixKrueger / TrimGalore
  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…
  ☆488Updated this week
• mikolmogorov / Flye
  De novo assembler for single molecule sequencing reads using repeat graphs
  ☆814Updated 6 months ago
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆409Updated 2 months ago
• deeptools / pyGenomeTracks
  python module to plot beautiful and highly customizable genome browser tracks
  ☆797Updated 8 months ago
• TransDecoder / TransDecoder
  TransDecoder source
  ☆285Updated 5 months ago
• fritzsedlazeck / Sniffles
  Structural variation caller using third generation sequencing
  ☆582Updated this week
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆394Updated this week
• lindenb / jvarkit
  Java utilities for Bioinformatics
  ☆495Updated last week
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆458Updated 2 weeks ago
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆288Updated last year
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆540Updated 8 months ago
• Illumina / strelka
  Strelka2 germline and somatic small variant caller
  ☆364Updated 3 years ago
• pachterlab / kallisto
  Near-optimal RNA-Seq quantification
  ☆673Updated 3 months ago
• ablab / quast
  Genome assembly evaluation tool
  ☆423Updated 4 months ago
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆337Updated 7 months ago
• nf-core / sarek
  Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
  ☆426Updated this week
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆221Updated 4 years ago
• NBISweden / AGAT
  Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/
  ☆490Updated last week
• chhylp123 / hifiasm
  Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
  ☆584Updated last month
• davidemms / OrthoFinder
  Phylogenetic orthology inference for comparative genomics
  ☆742Updated 4 months ago
• s-andrews / FastQC
  A quality control analysis tool for high throughput sequencing data
  ☆485Updated last year
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆400Updated 2 months ago
• jtamames / SqueezeMeta
  A complete pipeline for metagenomic analysis
  ☆398Updated this week