brentp / bwa-methView external linksLinks
fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
☆159Aug 8, 2025Updated 6 months ago
Alternatives and similar repositories for bwa-meth
Users that are interested in bwa-meth are comparing it to the libraries listed below
Sorting:
- A (mostly) universal methylation extractor for BS-seq experiments.☆176Jun 21, 2024Updated last year
- BISulfite-seq CUI Toolkit☆70Oct 9, 2025Updated 4 months ago
- Devel repository for bsseq☆39Feb 6, 2026Updated last week
- Abismal is a mapper of FASTQ bisulfite-converted short reads (between 50 and 1000 bases) to a FASTA reference genome.☆20Updated this week
- A tool to map bisulfite converted sequence reads and determine cytosine methylation states☆442Aug 8, 2025Updated 6 months ago
- Tools for working with SAM/BAM data☆605Dec 22, 2024Updated last year
- tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies☆180Dec 13, 2025Updated 2 months ago
- WALT is a read mapping program for bisulfite sequencing DNA methylation studies.☆17Aug 23, 2022Updated 3 years ago
- Software for predicting library complexity and genome coverage in high-throughput sequencing.☆94Dec 24, 2025Updated last month
- gemBS is a bioinformatics pipeline designed for high throughput analysis of DNA methylation from Whole Genome Bisulfite Sequencing data (…☆32Jan 28, 2022Updated 4 years ago
- SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data☆42Apr 7, 2022Updated 3 years ago
- R package for Inference of differentially methylated regions (DMRs) from bisulfite sequencing☆62May 9, 2025Updated 9 months ago
- SPP - R package for analysis of ChIP-seq and other functional sequencing data☆43Jul 6, 2021Updated 4 years ago
- ☆13Jun 24, 2019Updated 6 years ago
- ☆49Jan 4, 2023Updated 3 years ago
- ☆92Jan 11, 2022Updated 4 years ago
- DELLY2: Structural variant discovery by integrated paired-end and split-read analysis☆507Nov 6, 2025Updated 3 months ago
- Tools to process and analyze deep sequencing data.☆752Jul 23, 2025Updated 6 months ago
- A flexible framework for rapid genome analysis and interpretation☆319Oct 18, 2022Updated 3 years ago
- R package for DNA methylation analysis☆247Jan 18, 2026Updated 3 weeks ago
- make enriched heatmap which visualizes the enrichment of genomic signals to specific target regions.☆199Jan 30, 2026Updated 2 weeks ago
- Detecting sites of genomic enrichment☆198May 8, 2023Updated 2 years ago
- This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to…☆62Jul 20, 2020Updated 5 years ago
- Tools for next-generation sequencing analysis☆89Jun 25, 2019Updated 6 years ago
- The next version of bwa-mem☆817Oct 15, 2025Updated 4 months ago
- Microassembly based somatic variant caller for NGS data☆154Jun 23, 2022Updated 3 years ago
- Concordance and contamination estimator for tumor–normal pairs☆59Oct 22, 2024Updated last year
- Reference-based variant calling pipeline for a pair of phased haplotype assemblies☆105Jun 6, 2021Updated 4 years ago
- Structural Variation and fusion detection using targeted sequencing data from circulating cell free DNA☆29Jun 6, 2024Updated last year
- fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing☆822Updated this week
- A versatile aligning pipeline for bisulfite sequencing data☆66Oct 30, 2018Updated 7 years ago
- Simple FASTQ quality assessment using Python☆109May 22, 2021Updated 4 years ago
- Algorithm for detecting alternative splicing in a population of single cells. See details in Welch et al., Nucleic Acids Research 2016: h…☆23Jul 7, 2016Updated 9 years ago
- Updated and optimized fork of BSMAP☆23Dec 28, 2020Updated 5 years ago
- SALSA: A tool to scaffold long read assemblies with Hi-C data☆188May 17, 2024Updated last year
- A pipeline for analyzing DNA methylation data from bisulfite sequencing.☆71Oct 7, 2022Updated 3 years ago
- Scripts and notebooks used in Akgol Oksuz et al. paper☆11Jan 18, 2021Updated 5 years ago
- GEM-Mapper v3☆58Nov 25, 2025Updated 2 months ago
- Tools for bam file processing☆55Apr 20, 2015Updated 10 years ago