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.
  ☆176Updated last year
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆117Updated last year
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆143Updated 3 years ago
• tobiasrausch / alfred
  BAM Statistics, Feature Counting and Annotation
  ☆152Updated last month
• niu-lab / msisensor2
  Microsatellite instability (MSI) detection for tumor only data.
  ☆112Updated last year
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆175Updated last year
• kvittingseerup / IsoformSwitchAnalyzeR
  An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
  ☆121Updated last month
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆72Updated 5 years ago
• FelixKrueger / SNPsplit
  Allele-specific alignment sorting
  ☆61Updated 3 years ago
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆148Updated 4 months ago
• parklab / NGSCheckMate
  Software program for checking sample matching for NGS data
  ☆137Updated last year
• GoekeLab / sg-nex-data
  Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
  ☆148Updated 4 months ago
• mortazavilab / TALON
  Technology agnostic long read analysis pipeline for transcriptomes
  ☆155Updated last year
• xjtu-omics / msisensor-pro
  Microsatellite Instability (MSI) detection using high-throughput sequencing data.
  ☆115Updated 9 months ago
• mhammell-laboratory / TElocal
  A package for quantifying transposable elements at a locus level for RNAseq datasets.
  ☆31Updated 2 months ago
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated last year
• tderrien / FEELnc
  FEELnc : FlExible Extraction of LncRNA
  ☆93Updated 5 months ago
• CenterForMedicalGeneticsGhent / WisecondorX
  WisecondorX — An evolved WISECONDOR
  ☆109Updated last month
• harbourlab / SparK
  Publication quality NGS track plotting
  ☆117Updated 3 months ago
• griffithlab / regtools
  Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.
  ☆136Updated last year
• lh3 / hickit
  TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C
  ☆115Updated last week
• ding-lab / msisensor
  microsatellite instability detection using tumor only or paired tumor-normal data
  ☆132Updated 5 years ago
• AstraZeneca-NGS / reference_data
  Reference data: BED files, genes, transcripts, variations.
  ☆88Updated 8 years ago
• IARCbioinfo / BAM-tricks
  Tip and tricks for BAM files
  ☆86Updated 7 years ago
• BioinfoUNIBA / REDItools
  REDItools are python scripts to investigate RNA editing at genomic scale.
  ☆69Updated 6 months ago
• 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…
  ☆78Updated 5 years ago
• open2c / pairtools
  Extract 3D contacts (.pairs) from sequencing alignments
  ☆123Updated last week
• zhou-lab / biscuit
  BISulfite-seq CUI Toolkit
  ☆70Updated 3 months ago
• gatk-workflows / gatk4-exome-analysis-pipeline
  This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and In…
  ☆55Updated 5 years ago
• linsalrob / fastq-pair
  Match up paired end fastq files quickly and efficiently.
  ☆153Updated last year