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…
  ☆530Updated 2 months ago
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆472Updated last week
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆741Updated 3 months ago
• bwa-mem2 / bwa-mem2
  The next version of bwa-mem
  ☆792Updated last month
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆455Updated last year
• s-andrews / FastQC
  A quality control analysis tool for high throughput sequencing data
  ☆552Updated last week
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆491Updated last week
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆443Updated 10 months ago
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆434Updated 3 months ago
• CGATOxford / UMI-tools
  Tools for handling Unique Molecular Identifiers in NGS data sets
  ☆528Updated 4 months ago
• trinityrnaseq / trinityrnaseq
  Trinity RNA-Seq de novo transcriptome assembly
  ☆876Updated 9 months ago
• pachterlab / kallisto
  Near-optimal RNA-Seq quantification
  ☆708Updated 7 months ago
• fritzsedlazeck / Sniffles
  Structural variation caller using third generation sequencing
  ☆624Updated this week
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆760Updated 2 weeks ago
• lindenb / jvarkit
  Java utilities for Bioinformatics
  ☆511Updated last month
• usadellab / Trimmomatic
  ☆274Updated last month
• gmarcais / Jellyfish
  A fast multi-threaded k-mer counter
  ☆518Updated last year
• nservant / HiC-Pro
  HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
  ☆426Updated last year
• freebayes / freebayes
  Bayesian haplotype-based genetic polymorphism discovery and genotyping.
  ☆851Updated 5 months ago
• mikolmogorov / Flye
  De novo assembler for single molecule sequencing reads using repeat graphs
  ☆880Updated 6 months ago
• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆669Updated 4 months ago
• NBISweden / AGAT
  Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/
  ☆538Updated last month
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆555Updated last year
• Illumina / strelka
  Strelka2 germline and somatic small variant caller
  ☆387Updated 3 years ago
• Illumina / manta
  Structural variant and indel caller for mapped sequencing data
  ☆449Updated last month
• deeptools / pyGenomeTracks
  python module to plot beautiful and highly customizable genome browser tracks
  ☆847Updated last year
• biod / sambamba
  Tools for working with SAM/BAM data
  ☆596Updated 10 months ago
• aidenlab / juicer
  A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
  ☆466Updated 2 months ago
• davidemms / OrthoFinder
  Phylogenetic orthology inference for comparative genomics
  ☆811Updated 4 months ago
• Ensembl / ensembl-vep
  The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
  ☆509Updated this week