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
  ☆999Updated 7 months ago
• lindenb / jvarkit
  Java utilities for Bioinformatics
  ☆512Updated last month
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆513Updated last month
• Ensembl / ensembl-vep
  The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
  ☆506Updated this week
• Illumina / hap.py
  Haplotype VCF comparison tools
  ☆445Updated last year
• freebayes / freebayes
  Bayesian haplotype-based genetic polymorphism discovery and genotyping.
  ☆845Updated 4 months ago
• s-andrews / FastQC
  A quality control analysis tool for high throughput sequencing data
  ☆541Updated last week
• bwa-mem2 / bwa-mem2
  The next version of bwa-mem
  ☆785Updated 3 months ago
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆737Updated 2 months ago
• samtools / hts-specs
  Specifications of SAM/BAM and related high-throughput sequencing file formats
  ☆691Updated last month
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆756Updated 2 months ago
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆486Updated last month
• marbl / canu
  A single molecule sequence assembler for genomes large and small.
  ☆691Updated last month
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆454Updated last year
• trinityrnaseq / trinityrnaseq
  Trinity RNA-Seq de novo transcriptome assembly
  ☆874Updated 8 months ago
• cole-trapnell-lab / cufflinks
  ☆318Updated 5 years ago
• BenLangmead / bowtie2
  A fast and sensitive gapped read aligner
  ☆741Updated last month
• pachterlab / kallisto
  Near-optimal RNA-Seq quantification
  ☆702Updated 6 months ago
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆433Updated 2 months ago
• lh3 / seqtk
  Toolkit for processing sequences in FASTA/Q formats
  ☆1,498Updated 4 months ago
• Illumina / strelka
  Strelka2 germline and somatic small variant caller
  ☆383Updated 3 years ago
• COMBINE-lab / salmon
  🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
  ☆834Updated last year
• bcbio / bcbio-nextgen
  Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
  ☆1,016Updated last year
• igvteam / igv.js
  Embeddable genomic visualization component based on the Integrative Genomics Viewer
  ☆688Updated last week
• biod / sambamba
  Tools for working with SAM/BAM data
  ☆595Updated 9 months ago
• FelixKrueger / TrimGalore
  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…
  ☆524Updated last month
• Illumina / manta
  Structural variant and indel caller for mapped sequencing data
  ☆442Updated 2 years 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.
  ☆537Updated 4 months ago
• broadgsa / gatk
  Official code repository for GATK versions 1.0 through 3.7 (core engine). For GATK 4 code, see the https://github.com/broadinstitute/gatk…
  ☆295Updated 7 years ago
• 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…
  ☆855Updated 3 weeks ago