nextits
A pipeline for metabarcoding fungi and other eukaryotes with full-length ITS sequenced with PacBio
Science Score: 67.0%
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Links to: zenodo.org -
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Low similarity (10.9%) to scientific vocabulary
Keywords
Repository
A pipeline for metabarcoding fungi and other eukaryotes with full-length ITS sequenced with PacBio
Basic Info
- Host: GitHub
- Owner: vmikk
- License: apache-2.0
- Language: Nextflow
- Default Branch: main
- Homepage: https://next-its.github.io
- Size: 2.47 MB
Statistics
- Stars: 7
- Watchers: 2
- Forks: 0
- Open Issues: 2
- Releases: 5
Topics
Metadata Files
README.md
NextITS 
NextITS is an automated pipeline for metabarcoding fungi and other eukaryotes with full-length ITS sequenced with PacBio. Amplicons obtained with Illumina are also supported.
Introduction
The most widely used genetic markers for metabarcoding fungal communities are highly variable rRNA ITS1 and ITS2 sub-regions of the internal transcribed spacer. High-throughput metabarcoding has greatly improved our understanding of fungal community ecology. Here, we present NextITS, an automated pipeline for analyzing full-length ITS sequences (ITS1-5.8S-ITS2) from the Pacific Biosciences (PacBio) third-generation sequencing platform. Although the PacBio HiFi reads are highly accurate, the primary type of sequencing error is insertions or deletions in homopolymeric sites, which are also naturally common in fungal ITS. In the pipeline, we implemented correction of homopolymer errors, detection of tag-switching artefacts, and recovery of sequences false-positively annotated as chimeric. The pipeline is built using Nextflow workflow manager, with all the software dependencies packaged into Docker and Singularity containers.
User Documentation
User documentation: https://Next-ITS.github.io/
Quick Start
nextflow run vmikk/NextITS -r main \
-profile singularity \
-resume \
--input "pacbio_ccs.fastq.gz" \
--barcodes "sample_barcodes.fasta" \
--primer_forward "GTACACACCGCCCGTCG" \
--primer_reverse "CCTSCSCTTANTDATATGC" \
--its_region "full" \
--outdir "Results"
Citation
Mikryukov V., Anslan S., Tedersoo L. NextITS: a pipeline for metabarcoding fungi and other eukaryotes with full-length ITS sequenced with PacBio. https://github.com/vmikk/NextITS
Owner
- Name: Vladimir Mikryukov
- Login: vmikk
- Kind: user
- Location: Tartu, Estonia
- Company: The University of Tartu
- Twitter: vmikkkk
- Repositories: 54
- Profile: https://github.com/vmikk
Citation (CITATION.cff)
cff-version: 1.2.0 title: "NextITS: a pipeline for metabarcoding eukaryotes with full-length ITS sequenced with PacBio" type: software authors: - family-names: "Mikryukov" given-names: "Vladimir" orcid: "https://orcid.org/0000-0003-2786-2690" - family-names: "Anslan" given-names: "Sten" orcid: "https://orcid.org/0000-0002-2299-454X" - family-names: "Tedersoo" given-names: "Leho" orcid: "https://orcid.org/0000-0002-1635-1249" version: 1.0.0 doi: 10.5281/zenodo.15074881 date-released: 2025-03-24 url: "https://github.com/vmikk/NextITS" license: Apache-2.0 repository-code: "https://github.com/vmikk/NextITS"
GitHub Events
Total
- Create event: 1
- Release event: 1
- Issues event: 9
- Watch event: 2
- Issue comment event: 15
- Push event: 40
Last Year
- Create event: 1
- Release event: 1
- Issues event: 9
- Watch event: 2
- Issue comment event: 15
- Push event: 40
Committers
Last synced: 10 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Vladimir Mikryukov | v****v@g****m | 640 |
Issues and Pull Requests
Last synced: 4 months ago
All Time
- Total issues: 9
- Total pull requests: 0
- Average time to close issues: 5 days
- Average time to close pull requests: N/A
- Total issue authors: 3
- Total pull request authors: 0
- Average comments per issue: 2.56
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 4
- Pull requests: 0
- Average time to close issues: 2 days
- Average time to close pull requests: N/A
- Issue authors: 3
- Pull request authors: 0
- Average comments per issue: 2.5
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- splaisan (5)
- principezinho (2)
- XaviRoijals (1)