brentp / bwa-meth
fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
☆147Updated 5 months ago
Alternatives and similar repositories for bwa-meth:
Users that are interested in bwa-meth are comparing it to the libraries listed below
- A (mostly) universal methylation extractor for BS-seq experiments.☆169Updated 8 months ago
- Somatic copy number analysis using WGS paired end wholegenome sequencing☆70Updated 4 years ago
- phasing and Allele Specific Expression from RNA-seq☆111Updated 7 months ago
- Script to automatically create and run IGV snapshot batchscripts☆140Updated 2 years ago
- Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data☆157Updated 5 months ago
- Variant calling and somatic mutation/CNV detection for next-generation sequencing data☆156Updated last year
- ASCAT R package☆174Updated 2 months ago
- classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF☆211Updated 7 months ago
- Relevant papers for CNV and SV approaches☆94Updated 3 months ago
- This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are al…☆77Updated 4 years ago
- Microsatellite instability (MSI) detection for tumor only data.☆100Updated 9 months ago
- HiC uniform processing pipeline☆58Updated last year
- TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files☆128Updated 8 months ago
- VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.☆96Updated 9 months ago
- Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.☆96Updated 2 years ago
- Publication quality NGS track plotting☆111Updated 2 years ago
- An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)☆108Updated 2 weeks ago
- SV detection from paired end reads mapping☆117Updated 5 years ago
- Allele-specific alignment sorting☆54Updated 2 years ago
- Copy number calling and variant classification using targeted short read sequencing☆132Updated last month
- Software program for checking sample matching for NGS data☆128Updated 8 months ago
- HMMRATAC peak caller for ATAC-seq data☆100Updated 3 months ago
- Reference data: BED files, genes, transcripts, variations.☆82Updated 7 years ago
- Workflows for converting between sequence data formats☆38Updated 3 years ago
- STAR based ENCODE Long RNA-Seq processing pipeline☆93Updated 3 years ago
- nucleosome calling using ATAC-seq☆106Updated 4 years ago
- Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)☆141Updated last year
- Snakemake-based workflow for detecting structural variants in genomic data☆80Updated last week
- Bayesian genotyper for structural variants☆127Updated 3 years ago
- FEELnc : FlExible Extraction of LncRNA☆85Updated 5 months ago