nf-core/isoseq
Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed annotation.
Version history
- New entrypoint option to skip isoseq pre-processing.
- Update the pipeline to nf-core 2.14.1.
- Update modules.
- nf-validation version pinned PR25
- Upgrade from isoseq3 to isoseq (version 4) Fix segmentation fault PR27
- Add alternative entrypoint PR10
Added
- A new entreypoint system has been implemented to allow the user where to start the analysis.
- The
isoseqentrypoint runs the full pipeline. - The
mapentrypoint runs the pipeline from the mapping step. - This new
entreypointoption make possible to use the isoseq pipeline for analysis PacBio data when subreads are not provided, or for users who want to benefit from the mapping + TAMA analysis for their Nanopore data.
Fixed
-
Update modules to their nf-test version (bamtools/convert, custom/dumpsoftwareversions, gnu/sort, gstama/collapse/ gstama/merge, gstama/polyacleanup, gunzip, isoseq/refine, lima, minimap2/align, pbccs,ultra/align, ultra/index)
-
Since isoseq3 switch to version 4, it has been rename isoseq
Tool Previous version New version bamtools/convert 2.5.2 2.5.2 isoseq 3.8.2 4.0.0 lima 2.7.1 2.9.0 minimap2/align 2.24 2.28 gnu/sort 8.25 9.3 multiqc 1.21 1.24.1
-
Update the pipeline to nf-core 2.9.
-
Add gnu/sort to sort annotation before uLTRA index
-
Update citations
-
Add background to pipeline png
-
Update modules
Tool Previous version New version isoseq3 3.8.1 3.8.2 lima 2.6.0 2.7.1 bamtools/convert 2.5.1 2.5.2 gstama/merge 1.0.2 1.0.3 uLTRA/index 0.0.4.2 0.1 uLTRA/align 0.0.4.2 0.1 samtools 1.17 1.17 gnu/sort ---- 8.25
Fixed
- Update minimap2 path test: Don’t set gtf option. It is not expected to be used with minimap2 is chosen.
- FIX: Don’t prepare gtf channel when minimap2 is chosen.
Fixed
- Fix pipeline image path
- params.input invalid type if pipeline is run with local file in samplesheet (was working with URL)
Added
- Fix issue #17. Thanks to Husen M. Umer.
- Zenodo DOI
- Update to template v2.7.2
Fixed
- Remove hard coded capped option for GSTAMA_FILELIST step. Now follow user choice. Thanks to Mazdak Salavati.
Dependencies
| Tool | Previous version | New version |
|---|---|---|
| isoseq3 | 3.4.0 | 3.8.1 |
| lima | 2.2.0 | 2.6.0 |
| minimap2 | 2.21 | 2.24 |
| samtools | 1.12 | 1.14 |
| multiqc | 1.13 | 1.14 |
| pbccs | 6.2.0 | 6.4.0 |
| ultra_bioinformatics | 0.0.4 | 0.0.4.2 |
| samtools | 1.15.1 | 1.16.1 |
Update the pipeline to nf-core template v2.5.1. Update modules:
samplesheet_checkdumpsoftwareversionMultiQC
Fix aligner option documentation.
Pipeline performance improvement.
When uLTRA path is selected, It reduce computation by indexing GTF once instead of chunk times.
nf-core/isoseq is a bioinformatics best-practice analysis pipeline for Isoseq gene annotation with uLTRA and TAMA. Starting from raw isoseq subreads, the pipeline:
- Generates the Circular Consensus Sequences (CSS)
- Clean and polish CCS to create Full Length Non Chimeric (FLNC) reads
- Maps FLNCs on the genome
- Define and clean gene models