Alternatives and similar repositories for AWS-iGenomes

Users that are interested in AWS-iGenomes are comparing it to the libraries listed below

• CRG-CNAG / CalliNGS-NF
  GATK RNA-Seq Variant Calling in Nextflow
  ☆137Updated 2 years ago
• Zhong-Lab-UCSD / Genomic-Interactive-Visualization-Engine
  Genomic Interactive Visualization Engine
  ☆146Updated 2 years ago
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆148Updated 2 months ago
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆143Updated 2 years ago
• cbg-ethz / NGS-pipe
  NGS-pipe: next-generation sequencing pipelines for precision oncology
  ☆114Updated 6 years ago
• davetang / learning_vcf_file
  Learning the Variant Call Format
  ☆147Updated 4 months ago
• brentp / bwa-meth
  fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
  ☆153Updated 4 months ago
• ExpressionAnalysis / ea-utils
  Automatically exported from code.google.com/p/ea-utils
  ☆96Updated 2 years ago
• nf-core / smrnaseq
  A small-RNA sequencing analysis pipeline
  ☆98Updated this week
• Ensembl / VEP_plugins
  Plugins for the Ensembl Variant Effect Predictor (VEP)
  ☆162Updated last week
• nygenome / lancet
  Microassembly based somatic variant caller for NGS data
  ☆154Updated 3 years ago
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated last year
• griffithlab / regtools
  Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.
  ☆133Updated last year
• jdidion / atropos
  An NGS read trimming tool that is specific, sensitive, and speedy. (production)
  ☆126Updated 7 months ago
• AstraZeneca-NGS / reference_data
  Reference data: BED files, genes, transcripts, variations.
  ☆88Updated 8 years ago
• alimanfoo / pysamstats
  A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM …
  ☆194Updated last week
• gatk-workflows / gatk4-somatic-snvs-indels
  This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are al…
  ☆77Updated 5 years ago
• CCDG / Pipeline-Standardization
  ☆82Updated 7 years ago
• dpryan79 / MethylDackel
  A (mostly) universal methylation extractor for BS-seq experiments.
  ☆174Updated last year
• maasha / biopieces
  Biopieces is a bioinformatic framework of tools easily used and easily created.
  ☆144Updated 7 years ago
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆98Updated 3 years ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆165Updated 2 years ago
• sequana / sequana
  Sequana: a set of Snakemake NGS pipelines
  ☆151Updated 3 weeks ago
• SciLifeLab / NGI-RNAseq
  Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.
  ☆51Updated 7 years ago
• IARCbioinfo / BAM-tricks
  Tip and tricks for BAM files
  ☆86Updated 7 years ago
• htseq / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆107Updated 6 months ago
• nf-core / oncoanalyser
  A comprehensive cancer DNA/RNA analysis and reporting pipeline
  ☆97Updated this week
• gagneurlab / drop
  Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
  ☆157Updated 3 weeks ago
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆173Updated last year
• humanlongevity / HLA
  xHLA: Fast and accurate HLA typing from short read sequence data
  ☆113Updated 2 years ago