seandavi / GFFutils
Convert, explore, and manipulate GFF and GTF files (used in bioinformatics) using a sqlite-based approach
☆36Updated 14 years ago
Alternatives and similar repositories for GFFutils
Users that are interested in GFFutils are comparing it to the libraries listed below
Sorting:
- RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference…☆66Updated 2 years ago
- Python package and routines for merging VCF files☆29Updated 4 years ago
- MetaSV: An accurate and integrative structural-variant caller for next generation sequencing☆55Updated 7 years ago
- Adapter trimming and virtual library creation for Illumina Nextera Mate Pair libraries.☆54Updated 6 years ago
- Preprocessing tools for unique molecular index (UMI) sequencing reads☆31Updated 2 years ago
- MAGERI - Assemble, align and call variants for targeted genome re-sequencing with unique molecular identifiers☆21Updated 8 years ago
- utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.☆48Updated 6 years ago
- v2.x of the microassembly based somatic variant caller☆21Updated 2 weeks ago
- Suite of tools for analysing off-target reads to find CNVs, homozygous regions, and shared haplotypes☆29Updated 10 months ago
- Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata☆56Updated 3 years ago
- A set of tools to annotate VCF files with expression and readcount data☆29Updated 2 months ago
- Please consider using/contributing to https://github.com/nf-core/sarek☆40Updated 3 years ago
- QC3, a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.☆32Updated 8 years ago
- Benchmark pipeline for Structural Variation analyses, funded by the ALLBio.☆24Updated 10 years ago
- Pipeline for structural variant image curation and analysis.☆48Updated 3 years ago
- Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analyses☆31Updated 3 years ago
- Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model☆27Updated last year
- Prioritize structural variants based on CADD scores☆29Updated 5 years ago
- An awk-like VCF parser☆56Updated last year
- a Shiny/R application to view and annotate copy number variations☆27Updated 2 years ago
- CLAMMS is a scalable tool for detecting common and rare copy number variants from whole-exome sequencing data.☆29Updated 4 years ago
- SVsim: a tool that generates synthetic Structural Variant calls as benchmarks to test/evaluate SV calling pipelines.☆17Updated 7 years ago
- BigWig manpulation tools using libBigWig and htslib☆29Updated 9 months ago
- Exploration of controlled loss of quality values for compressing CRAM files☆34Updated 2 years ago
- BreakSeq2: Ultrafast and accurate nucleotide-resolution analysis of structural variants☆24Updated 9 years ago
- Personal diploid genome creation and coordinate conversion☆26Updated last month
- A snakemake pipeline for SV analysis from nanopore genome sequencing☆51Updated 5 years ago
- SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data☆42Updated 3 years ago
- filtering trio-based genetic variants in VCFs for clinical review☆21Updated 4 years ago
- Splice junction analysis and filtering from BAM files☆40Updated 3 years ago