Alternatives and similar repositories for igv

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

• arq5x / bedtools2
  bedtools - the swiss army knife for genome arithmetic
  ☆1,021Updated 10 months ago
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆525Updated last week
• freebayes / freebayes
  Bayesian haplotype-based genetic polymorphism discovery and genotyping.
  ☆862Updated 8 months ago
• s-andrews / FastQC
  A quality control analysis tool for high throughput sequencing data
  ☆578Updated last month
• samtools / hts-specs
  Specifications of SAM/BAM and related high-throughput sequencing file formats
  ☆696Updated 3 months ago
• Illumina / hap.py
  Haplotype VCF comparison tools
  ☆455Updated 2 years ago
• lindenb / jvarkit
  Java utilities for Bioinformatics
  ☆516Updated this week
• Ensembl / ensembl-vep
  The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
  ☆529Updated last week
• bwa-mem2 / bwa-mem2
  The next version of bwa-mem
  ☆814Updated 3 months ago
• marbl / canu
  A single molecule sequence assembler for genomes large and small.
  ☆697Updated 2 months ago
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆751Updated 6 months ago
• igvteam / igv.js
  Embeddable genomic visualization component based on the Integrative Genomics Viewer
  ☆707Updated 3 weeks ago
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆507Updated 3 months ago
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆768Updated last week
• BenLangmead / bowtie2
  A fast and sensitive gapped read aligner
  ☆769Updated last week
• biod / sambamba
  Tools for working with SAM/BAM data
  ☆605Updated last year
• trinityrnaseq / trinityrnaseq
  Trinity RNA-Seq de novo transcriptome assembly
  ☆881Updated last year
• mikolmogorov / Flye
  De novo assembler for single molecule sequencing reads using repeat graphs
  ☆900Updated 9 months ago
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆442Updated 6 months ago
• vcftools / vcftools
  A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.
  ☆550Updated 8 months ago
• gmarcais / Jellyfish
  A fast multi-threaded k-mer counter
  ☆529Updated last year
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆460Updated last year
• pysam-developers / pysam
  Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight…
  ☆877Updated last week
• fritzsedlazeck / Sniffles
  Structural variation caller using third generation sequencing
  ☆634Updated last month
• deeptools / pyGenomeTracks
  python module to plot beautiful and highly customizable genome browser tracks
  ☆862Updated last year
• rrwick / Bandage
  a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
  ☆666Updated 3 years ago
• aidenlab / juicer
  A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
  ☆474Updated 5 months ago
• pachterlab / kallisto
  Near-optimal RNA-Seq quantification
  ☆720Updated 2 weeks ago
• nanopore-wgs-consortium / NA12878
  Data and analysis for NA12878 genome on nanopore
  ☆401Updated 3 years ago
• lh3 / seqtk
  Toolkit for processing sequences in FASTA/Q formats
  ☆1,526Updated 8 months ago