A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies
☆35Jun 30, 2024Updated last year
Alternatives and similar repositories for ngs-preprocess
Users that are interested in ngs-preprocess are comparing it to the libraries listed below
Sorting:
- Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads☆64Jan 22, 2026Updated last month
- Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data☆13Jun 12, 2024Updated last year
- Add biological annotations to variants in a given VCF file.☆32Sep 13, 2021Updated 4 years ago
- A pipeline for high-quality bacterial genome construction using ONT sequencing☆38Sep 22, 2022Updated 3 years ago
- UPHL's Reference Free Pipeline☆27Updated this week
- Customer workshop materials☆19May 11, 2023Updated 2 years ago
- The Whole Genome Sequencing Coverage Plot (wgscovplot) is a tool to generate HTML Interactive Coverage Plot given coverage depth informat…☆19May 3, 2024Updated last year
- Finding regions of similarity between plasmids☆17Nov 2, 2022Updated 3 years ago
- ViromeScan allows the user to explore and taxonomically characterize the virome from metagenomic reads, efficiently denoising samples fro…☆13Feb 13, 2023Updated 3 years ago
- ☆27Aug 2, 2023Updated 2 years ago
- A simple fastp-MultiQC nextflow pipeline☆12Feb 2, 2023Updated 3 years ago
- seqfu - Sequece Fastx Utilities☆126Jan 31, 2026Updated last month
- hAMRoaster is an analysis pipeline that can compare the output of tools for detecting AMR genes and provide metrics of their performance☆22Mar 8, 2024Updated last year
- Nextflow workflow for automatic repeat detection, classification and masking☆13Feb 19, 2018Updated 8 years ago
- Command line utility for working with next-generation sequencing files.☆38Jun 24, 2025Updated 8 months ago
- Repeat and haplotype aware error correction in nanopore sequencing reads with DeChat☆25May 10, 2025Updated 9 months ago
- Correcting errors in noisy long reads using variation graphs☆50Nov 17, 2022Updated 3 years ago
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆38Feb 20, 2026Updated last week
- Removing PCR duplicates for sequencing reads.☆14Sep 8, 2020Updated 5 years ago
- Cookiecutter profile for making a NextFlow-based bioinformatics tool☆17Jul 8, 2024Updated last year
- Hierarchical binned indexed data store for on-disk genomic data.☆13Jan 18, 2025Updated last year
- A collection of Groovy classes that provide utility services to nextflow pipelines.☆13Oct 25, 2022Updated 3 years ago
- Robust individual and aggregate checksums for nucleotide sequences☆17Feb 8, 2026Updated 3 weeks ago
- CLI to automate Nextflow pipeline testing☆12Dec 15, 2025Updated 2 months ago
- mreps: software for tandem repeat identification in DNA☆15Nov 13, 2019Updated 6 years ago
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, es…☆42Aug 5, 2024Updated last year
- Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.☆105Jan 22, 2026Updated last month
- Read contamination removal☆25Jan 24, 2024Updated 2 years ago
- add true-negative SVs from a population callset to a truth-set.☆15Jun 17, 2022Updated 3 years ago
- Nextflow DSL2 pipeline to generate data for a BlobToolKit analysis. This workflow is part of the Tree of Life production suite.☆15Feb 12, 2026Updated 2 weeks ago
- Plot multiple sequence alignment (MSA)☆16Sep 23, 2024Updated last year
- Automated Detection and Qualification of Differential Methylation☆16Nov 21, 2023Updated 2 years ago
- ☆14Jun 30, 2021Updated 4 years ago
- A repo with just adapter sequences☆15Jul 7, 2025Updated 7 months ago
- STRspy: a novel alignment and quantification-based state-of-the-art method, short tandem repeat (STR) detection calling tool designed spe…☆18Feb 21, 2026Updated last week
- General purpose utility related to GAF files☆29Jan 27, 2026Updated last month
- ⛰ covtobed | Convert the coverage track from a BAM file into a BED file☆44Nov 6, 2025Updated 3 months ago
- Experimental plugin to integrate GPT like prompt into Nextflow☆17Apr 15, 2024Updated last year
- PAF (pairwise alignment format) validator based on extended CIGAR strings☆15Aug 10, 2025Updated 6 months ago