Alternatives and similar repositories for bwa-meth

Users that are interested in bwa-meth are comparing it to the libraries listed below

• dpryan79 / MethylDackel
  A (mostly) universal methylation extractor for BS-seq experiments.
  ☆172Updated last year
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆116Updated last year
• griffithlab / regtools
  Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.
  ☆131Updated last year
• parklab / NGSCheckMate
  Software program for checking sample matching for NGS data
  ☆134Updated last year
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆142Updated 2 years ago
• niu-lab / msisensor2
  Microsatellite instability (MSI) detection for tumor only data.
  ☆109Updated last year
• mortazavilab / TALON
  Technology agnostic long read analysis pipeline for transcriptomes
  ☆149Updated last year
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆93Updated 10 months ago
• GoekeLab / sg-nex-data
  Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
  ☆135Updated 3 weeks ago
• kvittingseerup / IsoformSwitchAnalyzeR
  An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
  ☆117Updated 7 months ago
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆147Updated last week
• AstraZeneca-NGS / reference_data
  Reference data: BED files, genes, transcripts, variations.
  ☆85Updated 7 years ago
• harbourlab / SparK
  Publication quality NGS track plotting
  ☆114Updated 3 years ago
• tobiasrausch / alfred
  BAM Statistics, Feature Counting and Annotation
  ☆149Updated this week
• mhammell-laboratory / TElocal
  A package for quantifying transposable elements at a locus level for RNAseq datasets.
  ☆29Updated 7 months ago
• tderrien / FEELnc
  FEELnc : FlExible Extraction of LncRNA
  ☆90Updated last month
• xjtu-omics / msisensor-pro
  Microsatellite Instability (MSI) detection using high-throughput sequencing data.
  ☆111Updated 5 months ago
• BioinfoUNIBA / REDItools
  REDItools are python scripts to investigate RNA editing at genomic scale.
  ☆68Updated last month
• zhou-lab / biscuit
  BISulfite-seq CUI Toolkit
  ☆66Updated 8 months ago
• MonashBioinformaticsPlatform / RSeQC
  fork of RSeQC python RNAseq metrics suit of tools
  ☆49Updated 6 years ago
• zhxiaokang / RASflow
  RNA-Seq analysis workflow
  ☆104Updated 4 years ago
• signalbash / how_are_we_stranded_here
  Check strandedness of RNA-Seq fastq files
  ☆125Updated 3 years ago
• IARCbioinfo / BAM-tricks
  Tip and tricks for BAM files
  ☆86Updated 7 years ago
• Zhong-Lab-UCSD / Genomic-Interactive-Visualization-Engine
  Genomic Interactive Visualization Engine
  ☆145Updated 2 years ago
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆170Updated last year
• FelixKrueger / SNPsplit
  Allele-specific alignment sorting
  ☆58Updated 2 years ago
• BioinfoUNIBA / REDItools2
  ☆58Updated last month
• parklab / ShatterSeek
  ☆72Updated 2 years ago
• a2iEditing / RNAEditingIndexer
  A tool for the calculation of RNA-editing index for RNA seq data
  ☆43Updated last year
• ucagenomix / sicelore
  Single Cell Long Read is a suite of tools dedicated to Cell barcode / UMI assignment and analysis of highly multiplexed single cell Nanop…
  ☆75Updated 2 years ago