nf-core / sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
☆410Updated this week
Related projects ⓘ
Alternatives and complementary repositories for sarek
- A tool to map bisulfite converted sequence reads and determine cytosine methylation states☆393Updated last week
- RNA-seq workflow using STAR and DESeq2☆327Updated 3 months ago
- A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…☆472Updated last month
- Fast genome-wide functional annotation through orthology assignment☆572Updated 6 months ago
- Customizable workflows based on snakemake and python for the analysis of NGS data☆389Updated this week
- Another Gtf/Gff Analysis Toolkit☆464Updated last month
- ATAC-seq peak-calling and QC analysis pipeline☆188Updated this week
- Collections of library structure and sequence of popular single cell genomic methods☆437Updated 2 weeks ago
- Plot structural variant signals from many BAMs and CRAMs☆530Updated 4 months ago
- ENCODE ATAC-seq pipeline☆391Updated 4 months ago
- Tools to process and analyze deep sequencing data.☆684Updated this week
- ChIP-seq peak-calling, QC and differential analysis pipeline.☆195Updated this week
- parallel fastq-dump wrapper☆283Updated last year
- HiC-Pro: An optimized and flexible pipeline for Hi-C data processing☆386Updated 7 months ago
- Intro to ChIPseq using HPC☆289Updated last year
- RSEM: accurate quantification of gene and isoform expression from RNA-Seq data☆421Updated 8 months ago
- Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.☆351Updated 2 months ago
- A tool to find sequencing data and metadata from public databases.☆552Updated 3 months ago
- Tools for handling Unique Molecular Identifiers in NGS data sets☆493Updated last month
- Transcript assembly and quantification for RNA-Seq☆384Updated last week
- ☆221Updated 5 months ago
- Fast and accurate gene fusion detection from RNA-Seq data☆227Updated 3 weeks ago
- Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms☆375Updated 4 months ago
- python module to plot beautiful and highly customizable genome browser tracks☆775Updated 4 months ago
- GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more☆376Updated last year
- ☆375Updated 2 years ago
- GTEx & TOPMed data production and analysis pipelines☆342Updated 7 months ago
- MACS -- Model-based Analysis of ChIP-Seq☆714Updated last week
- RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.☆923Updated 2 weeks ago
- Structural variation caller using third generation sequencing☆561Updated last week