daler / pybedtools
Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
☆311Updated last month
Alternatives and similar repositories for pybedtools:
Users that are interested in pybedtools are comparing it to the libraries listed below
- HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.☆123Updated 4 years ago
- This Snakemake pipeline implements the GATK best-practices workflow☆247Updated last year
- tools for adding mutations to existing .bam files, used for testing mutation callers☆237Updated 3 months ago
- GFF and GTF file manipulation and interconversion☆293Updated 10 months ago
- Plot structural variant signals from many BAMs and CRAMs☆538Updated 7 months ago
- Package for fetching metadata and downloading data from SRA/ENA/GEO☆320Updated 3 months ago
- SUPPA: Fast quantification of splicing and differential splicing☆268Updated 7 months ago
- BEDOPS: high-performance genomic feature operations☆310Updated last year
- Count bases in BAM/CRAM files☆312Updated 3 years ago
- annotate a VCF with other VCFs/BEDs/tabixed files☆369Updated last year
- Variant calling and somatic mutation/CNV detection for next-generation sequencing data☆156Updated last year
- ☆262Updated this week
- Extension for Jupyter which integrates igv.js☆153Updated 2 years ago
- Performant Pythonic GenomicRanges☆453Updated 8 months ago
- VarDict☆192Updated last year
- Quick mining and visualization of NGS data by integrating genomic databases☆263Updated last year
- parallel fastq-dump wrapper☆287Updated last year
- Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae …☆212Updated 8 months ago
- This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.☆238Updated 2 years ago
- RTG Tools: Utilities for accurate VCF comparison and manipulation☆306Updated 8 months ago
- Bayesian haplotype-based mutation calling☆307Updated last year
- A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM …☆194Updated 2 weeks ago
- Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls☆198Updated 3 years ago
- GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more☆395Updated last month
- HiC-Pro: An optimized and flexible pipeline for Hi-C data processing☆394Updated 10 months ago
- Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data☆209Updated 4 years ago
- C++ API & command-line toolkit for working with BAM data☆423Updated 7 months ago
- Miscellaneous collection of Python and R scripts for processing Iso-Seq data☆261Updated last year
- Customizable workflows based on snakemake and python for the analysis of NGS data☆392Updated this week
- GRIDSS: the Genomic Rearrangement IDentification Software Suite☆265Updated last year