Alternatives and similar repositories for Bismark:

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

• FelixKrueger / TrimGalore
  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…
  ☆500Updated last month
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆433Updated last week
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆253Updated last year
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆339Updated 8 months ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆541Updated 9 months ago
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆438Updated last year
• hbctraining / Intro-to-ChIPseq
  Intro to ChIPseq using HPC
  ☆302Updated 2 years ago
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆290Updated 2 years ago
• nf-core / chipseq
  ChIP-seq peak-calling, QC and differential analysis pipeline.
  ☆211Updated last month
• mskcc / vcf2maf
  Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
  ☆386Updated 4 months ago
• usadellab / Trimmomatic
  ☆241Updated 10 months ago
• nservant / HiC-Pro
  HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
  ☆402Updated last year
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆238Updated last month
• TransDecoder / TransDecoder
  TransDecoder source
  ☆288Updated 6 months ago
• shenlab-sinai / ngsplot
  Quick mining and visualization of NGS data by integrating genomic databases
  ☆264Updated last year
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆274Updated 10 months ago
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆299Updated 4 years ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆265Updated last year
• sdparekh / zUMIs
  zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
  ☆279Updated 9 months ago
• WGLab / doc-ANNOVAR
  Documentation for the ANNOVAR software
  ☆243Updated last month
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆396Updated last week
• Xinglab / rmats-turbo
  ☆252Updated 5 months ago
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆246Updated 2 months ago
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆462Updated last month
• nf-core / atacseq
  ATAC-seq peak-calling and QC analysis pipeline
  ☆200Updated last month
• saketkc / pysradb
  Package for fetching metadata and downloading data from SRA/ENA/GEO
  ☆326Updated 2 months ago
• dpryan79 / ChromosomeMappings
  This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.
  ☆241Updated 2 years ago
• Illumina / strelka
  Strelka2 germline and somatic small variant caller
  ☆366Updated 3 years ago
• igvteam / igv-reports
  Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
  ☆361Updated 4 months ago
• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆610Updated 11 months ago