snakemake-workflows / dna-seq-gatk-variant-callingLinks
This Snakemake pipeline implements the GATK best-practices workflow
☆262Updated 2 years ago
Alternatives and similar repositories for dna-seq-gatk-variant-calling
Users that are interested in dna-seq-gatk-variant-calling are comparing it to the libraries listed below
Sorting:
- Plot structural variant signals from many BAMs and CRAMs☆557Updated last year
- Fast and accurate gene fusion detection from RNA-Seq data☆258Updated 3 months ago
- Miscellaneous collection of Python and R scripts for processing Iso-Seq data☆279Updated 2 years ago
- Annotation and Ranking of Structural Variation☆281Updated 3 months ago
- Full-Length Alternative Isoform analysis of RNA☆246Updated last week
- Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.☆398Updated 2 months ago
- parallel fastq-dump wrapper☆302Updated 2 years ago
- RNA-seq workflow using STAR and DESeq2☆351Updated 3 weeks ago
- Count bases in BAM/CRAM files☆322Updated 3 years ago
- Variant calling and somatic mutation/CNV detection for next-generation sequencing data☆165Updated 2 years ago
- Documentation for the ANNOVAR software☆246Updated 5 months ago
- Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads☆229Updated 6 months ago
- classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF☆254Updated 6 months ago
- This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.☆245Updated 3 years ago
- A package for including transposable elements in differential enrichment analysis of sequencing datasets.☆275Updated 2 months ago
- PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.☆284Updated 11 months ago
- (Not Offical) BBMap short read aligner, and other bioinformatic tools.☆244Updated 4 years ago
- SUPPA: Fast quantification of splicing and differential splicing☆292Updated 2 months ago
- Tool for the Quality Control of Long-Read Defined Transcriptomes☆251Updated 2 weeks ago
- Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark/bwa-meth + MethylDackel or bwa-mem + rastair☆185Updated this week
- TransDecoder source☆301Updated 3 months ago
- Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools☆160Updated 3 years ago
- Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms☆407Updated 5 months ago
- Read trimming tool for Illumina NGS data.☆149Updated 10 years ago
- STAR-Fusion codebase☆246Updated 3 months ago
- Nanopore demultiplexing, QC and alignment pipeline☆218Updated last month
- GRIDSS: the Genomic Rearrangement IDentification Software Suite☆280Updated 7 months ago
- Structural variant toolkit for VCFs☆394Updated last month
- Quick mining and visualization of NGS data by integrating genomic databases☆268Updated 2 years ago
- Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.☆288Updated 4 months ago