Alternatives and similar repositories for hisat

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

• macarthur-lab / igv_utils
  utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.
  ☆49Updated 6 years ago
• kingsfordgroup / sailfish
  Rapid Mapping-based Isoform Quantification from RNA-Seq Reads
  ☆126Updated 3 years ago
• gt1 / biobambam2
  Tools for early stage alignment file processing
  ☆95Updated 6 years ago
• aryeelab / umi
  Preprocessing tools for unique molecular index (UMI) sequencing reads
  ☆31Updated 2 years ago
• arq5x / cyvcf
  A fast Python library for VCF files leveraging Cython for speed.
  ☆52Updated 7 years ago
• KHP-Informatics / ngseasy
  Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)
  ☆86Updated 8 years ago
• lh3 / fermikit
  De novo assembly based variant calling pipeline for Illumina short reads
  ☆108Updated 4 years ago
• ngsutils / ngsutils
  Tools for next-generation sequencing analysis
  ☆89Updated 6 years ago
• COMBINE-lab / RapMap
  Rapid sensitive and accurate read mapping via quasi-mapping
  ☆89Updated 5 years ago
• arq5x / grabix
  a wee tool for random access into BGZF files.
  ☆85Updated 7 years ago
• IARCbioinfo / needlestack
  Multi-sample somatic variant caller
  ☆52Updated 3 years ago
• pachterlab / kma
  Keep Me Around: Intron Retention Detection
  ☆29Updated 6 years ago
• mozack / abra
  Assembly Based ReAligner
  ☆74Updated 7 years ago
• boutroslab / cld
  A software for the multispecies design of CRISPR/Cas9 libraries
  ☆36Updated 2 years ago
• BD2KGenomics / toil-scripts
  Toil workflows for common genomic pipelines
  ☆33Updated 5 years ago
• cc2qe / vawk
  An awk-like VCF parser
  ☆56Updated last year
• lh3 / CHM-eval
  ☆54Updated 5 years ago
• relipmoc / skewer
  ☆95Updated 2 years ago
• nellore / rail
  Scalable RNA-seq analysis
  ☆73Updated 4 years ago
• PapenfussLab / socrates
  ☆16Updated 8 years ago
• lh3 / fermi-lite
  Standalone C library for assembling Illumina short reads in small regions
  ☆72Updated 2 years ago
• nellore / intropolis
  Exon-exon splice junctions across SRA
  ☆42Updated 4 years ago
• Oshlack / STRetch
  Method for detecting STR expansions from short-read sequencing data
  ☆63Updated 3 years ago
• dpryan79 / libBigWig
  A C library for handling bigWig files
  ☆81Updated 8 months ago
• gogetdata / ggd-recipes
  conda recipes for genomic data
  ☆84Updated 4 years ago
• bioinform / varsim
  VarSim: A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications
  ☆89Updated 11 months ago
• Cibiv / Teaser
  A tool to benchmark mappers and different parameters within minutes
  ☆44Updated 6 years ago
• walaj / bxtools
  Tools for analyzing 10X Genomics data
  ☆42Updated 6 years ago
• dcjones / fastq-tools
  Small utilities for working with fastq sequence files.
  ☆123Updated 2 years ago
• JohnLonginotto / pybam
  Very simple, pure python, BAM file reader
  ☆79Updated 6 years ago