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short-reads

Here are 5 public repositories matching this topic...

nf-cmgg / structural

A bioinformatics best-practice analysis pipeline for calling structural variants (SVs), copy number variants (CNVs) and repeat region expansions (RREs) from short DNA reads

annotation repeats ngs cnv cram structural-variation ngs-pipeline nextflow-pipeline short-reads

Updated Feb 4, 2025
Nextflow

nf-core / detaxizer

A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Removal is optional.

workflow nanopore pipeline nextflow shotgun filter metagenomics edna microbiome fastq metabarcoding long-reads taxonomic-classification de-identification nf-core short-reads taxonomic-profiling decontamination

Updated Jan 27, 2025
Nextflow

nf-cmgg / germline

A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data

annotation ngs germline cram ngs-pipeline genotyping germline-variant-calling short-reads

Updated Feb 4, 2025
Nextflow

digenoma-lab / alnsl

Nextflow pipeline for short-read alignment

nextflow mapping illumina mgi short-reads

Updated May 25, 2023
Nextflow

digenoma-lab / nf-mag-depths

A nextflow pipeline to calculate depth of coverage from a metagenomic set of bins

coverage bioinformatics metagenomics short-reads

Updated Jul 11, 2024
Nextflow

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