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
• gt1 / biobambam2
  Tools for early stage alignment file processing
  ☆95Updated 6 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
• IARCbioinfo / needlestack
  Multi-sample somatic variant caller
  ☆52Updated 3 years ago
• KHP-Informatics / ngseasy
  Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)
  ☆86Updated 8 years ago
• arq5x / cyvcf
  A fast Python library for VCF files leveraging Cython for speed.
  ☆52Updated 7 years ago
• nellore / rail
  Scalable RNA-seq analysis
  ☆73Updated 4 years ago
• mozack / abra
  Assembly Based ReAligner
  ☆74Updated 7 years ago
• pachterlab / kma
  Keep Me Around: Intron Retention Detection
  ☆29Updated 6 years ago
• nellore / intropolis
  Exon-exon splice junctions across SRA
  ☆42Updated 4 years ago
• kingsfordgroup / sailfish
  Rapid Mapping-based Isoform Quantification from RNA-Seq Reads
  ☆127Updated 3 years ago
• aryeelab / umi
  Preprocessing tools for unique molecular index (UMI) sequencing reads
  ☆31Updated 2 years ago
• BD2KGenomics / toil-scripts
  Toil workflows for common genomic pipelines
  ☆33Updated 6 years ago
• lh3 / fermikit
  De novo assembly based variant calling pipeline for Illumina short reads
  ☆109Updated 4 years ago
• relipmoc / skewer
  ☆95Updated 3 years ago
• boutroslab / cld
  A software for the multispecies design of CRISPR/Cas9 libraries
  ☆36Updated 3 years ago
• hartleys / QoRTs
  Quality of RNA-Seq Toolset
  ☆53Updated 6 years ago
• lh3 / bgt
  Flexible genotype query among 30,000+ samples whole-genome
  ☆94Updated 6 years ago
• arq5x / grabix
  a wee tool for random access into BGZF files.
  ☆85Updated 7 years ago
• arq5x / bedtools-protocols
  ☆78Updated 11 years ago
• Ettwiller / Damage-estimator
  Estimate damage in standard NGS library preparation. Incompatible with library preparation methods from which the imbalance is lost (such…
  ☆54Updated 8 years ago
• pmelsted / pizzly
  Fast fusion detection using kallisto
  ☆79Updated 4 months ago
• schatzlab / appliedgenomics2017
  JHU EN.600.649: Computational Genomics: Applied Comparative Genomics
  ☆58Updated 7 years ago
• roryk / tiny-test-data
  Super small biological datasets for unit testing
  ☆61Updated 5 years ago
• jdidion / atropos
  An NGS read trimming tool that is specific, sensitive, and speedy. (production)
  ☆125Updated 6 months ago
• bioinform / varsim
  VarSim: A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications
  ☆90Updated last year
• genome / somatic-sniper
  A tool to call somatic single nucleotide variants.
  ☆41Updated 10 years ago
• CGATOxford / cgat
  Do not use - please refer to our newest code: https://github.com/cgat-developers/cgat-apps
  ☆124Updated 6 years ago
• dpryan79 / libBigWig
  A C library for handling bigWig files
  ☆81Updated 9 months ago