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
  ☆977Updated last month
• Ensembl / ensembl-vep
  The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
  ☆477Updated 2 weeks ago
• bwa-mem2 / bwa-mem2
  The next version of bwa-mem
  ☆748Updated 8 months ago
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆730Updated last week
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆499Updated 5 months ago
• biod / sambamba
  Tools for working with SAM/BAM data
  ☆583Updated 3 months ago
• s-andrews / FastQC
  A quality control analysis tool for high throughput sequencing data
  ☆494Updated last year
• lindenb / jvarkit
  Java utilities for Bioinformatics
  ☆497Updated last week
• Illumina / hap.py
  Haplotype VCF comparison tools
  ☆426Updated last year
• mikolmogorov / Flye
  De novo assembler for single molecule sequencing reads using repeat graphs
  ☆825Updated 7 months ago
• pachterlab / kallisto
  Near-optimal RNA-Seq quantification
  ☆675Updated last week
• rrwick / Bandage
  a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
  ☆610Updated 2 years ago
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆714Updated 2 weeks ago
• marbl / canu
  A single molecule sequence assembler for genomes large and small.
  ☆674Updated last week
• freebayes / freebayes
  Bayesian haplotype-based genetic polymorphism discovery and genotyping.
  ☆820Updated last month
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆462Updated last month
• lh3 / seqtk
  Toolkit for processing sequences in FASTA/Q formats
  ☆1,452Updated 8 months ago
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆415Updated 3 months ago
• MultiQC / MultiQC
  Aggregate results from bioinformatics analyses across many samples into a single report.
  ☆1,288Updated this week
• CGATOxford / UMI-tools
  Tools for handling Unique Molecular Identifiers in NGS data sets
  ☆507Updated last month
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆438Updated last year
• nf-core / sarek
  Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
  ☆440Updated this week
• ablab / quast
  Genome assembly evaluation tool
  ☆427Updated 5 months ago
• pcingola / SnpEff
  ☆268Updated 2 months ago
• DerrickWood / kraken2
  The second version of the Kraken taxonomic sequence classification system
  ☆778Updated this week
• samtools / hts-specs
  Specifications of SAM/BAM and related high-throughput sequencing file formats
  ☆673Updated this week
• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆609Updated 11 months ago
• tanghaibao / jcvi
  Python library to facilitate genome assembly, annotation, and comparative genomics
  ☆813Updated last week
• mdshw5 / pyfaidx
  Efficient pythonic random access to fasta subsequences
  ☆468Updated 6 months ago
• Illumina / strelka
  Strelka2 germline and somatic small variant caller
  ☆366Updated 3 years ago