nf-core / sarekLinks
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
☆541Updated last week
Alternatives and similar repositories for sarek
Users that are interested in sarek are comparing it to the libraries listed below
Sorting:
- A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…☆539Updated 2 weeks ago
- MACS -- Model-based Analysis of ChIP-Seq☆768Updated last week
- Transcript assembly and quantification for RNA-Seq☆485Updated last month
- A tool to map bisulfite converted sequence reads and determine cytosine methylation states☆442Updated 6 months ago
- Plot structural variant signals from many BAMs and CRAMs☆558Updated last year
- The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants☆530Updated last week
- Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/☆556Updated 3 weeks ago
- ChIP-seq peak-calling, QC and differential analysis pipeline.☆230Updated 2 months ago
- A quality control analysis tool for high throughput sequencing data☆578Updated last month
- Tools for handling Unique Molecular Identifiers in NGS data sets☆536Updated last week
- RNA-seq workflow using STAR and DESeq2☆351Updated last month
- GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more☆457Updated last year
- RSEM: accurate quantification of gene and isoform expression from RNA-Seq data☆460Updated last year
- Customizable workflows based on snakemake and python for the analysis of NGS data☆397Updated 2 weeks ago
- Tools to process and analyze deep sequencing data.☆752Updated 6 months ago
- Structural variant and indel caller for mapped sequencing data☆458Updated 4 months ago
- The second version of the Kraken taxonomic sequence classification system☆866Updated last week
- Haplotype VCF comparison tools☆455Updated 2 years ago
- An accurate GFF3/GTF lift over pipeline☆525Updated 2 years ago
- Structural variation caller using third generation sequencing☆634Updated last month
- Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.☆398Updated last week
- This Snakemake pipeline implements the GATK best-practices workflow☆262Updated 2 years ago
- DELLY2: Structural variant discovery by integrated paired-end and split-read analysis☆507Updated 3 months ago
- The next version of bwa-mem☆816Updated 3 months ago
- parallel fastq-dump wrapper☆303Updated 2 years ago
- ☆286Updated 3 months ago
- HiC-Pro: An optimized and flexible pipeline for Hi-C data processing☆430Updated last year
- python module to plot beautiful and highly customizable genome browser tracks☆862Updated last year
- Near-optimal RNA-Seq quantification☆720Updated 3 weeks ago
- Miscellaneous collection of Python and R scripts for processing Iso-Seq data☆278Updated 2 years ago