nf-core/pairgenomealign
Pairwise genome comparison pipeline using the LAST software to align a list of query genomes to a target genome, and plot the results
comparative-genomicsdot-plotgenomicslastpairwise-alignmentsyntenywhole-genome-alignment
Version history
v2.2.0 “Chagara ponzu” - [May 29th 2025]
Added
- Support for export to BAM and CRAM formats (#31) (#43).
- SAM/BAM/CRAM alignments files are sorted and their header features all sequences of the target genome.
- Report ungapped percent identity (#46).
- Update full-size test genomes to feature more T2T assemblies (#59).
- Use a single mulled container for LAST, Samtools and open-fonts, to save ~280 Mb of downloads (#58).
- Allow export to multiple formats (comma-separated list) (#42).
- Allow skipping of the assembly QC with
--skip_assembly_qc(#53).
Dependencies
| Dependency | Old version | New version |
|---|---|---|
SAMTOOLS_BGZIP | 1.21 | |
SAMTOOLS_DICT | 1.21 | |
SAMTOOLS_FAIDX | 1.21 |
Parameters
| Old parameter | New parameter |
|---|---|
--skip_assembly_qc |
Fixed
- Remove noisy tag in the
MULTIQC_ASSEMBLYSCAN_PLOT_DATAlocal module (#64). - Restore BED format support (#56).
- Document the
multiqc_train.txtandmultiqc_last_o2o.txtaggregating alignment statistics (#52). - Point the test configs samplesheets to
nf-core/test-datasetsin order to run the AWS full tests (#62). - Update metro map, in white background (#71).
- Removed the
last/mafswapmodule, which was actually not used.
v2.1.0 “Goya champuru” - [May 16th 2025]
Added
- New
--dotplot_filterparamater to produce extra alignment plots where small off-diagonal signal is filtered out (#35). - New
--dotplot_width,--dotplot_heightand--dotplot_font_sizeparameters to control alignment plot size (#38).
Fixed
- In alignment plots, contig names are now written with a nice scalable font instead of being pixellised (#44).
- Conforms to nf-core template version 3.2.1 (#54).
- Removed some old linting exceptions.
- Removed the
gfastatsmodules, which was actually not used. - Make sure the subworkflows collect all module versions.
- Fix plot IDs for comptatibility with MultiQC 1.28.
Parameters
| Old parameter | New parameter |
|---|---|
--dotplot_filter | |
--dotplot_font_size | |
--dotplot_height | |
--dotplot_width |
Dependencies
| Dependency | Old version | New version |
|---|---|---|
LAST | 1608 | 1611 |
MultiQC | 1.27 | 1.28 |
v2.0.0 “Naga imo” - [February 5th, 2025]
Breaking changes
- The LAST software was updated and it has new defaults for some of its parameters. The alignments ran with this pipeline will not be identical to the ones from older versions.
Added
- The
alignment/lastdbdirectory is not output anymore. It consumed space, is not usually needed for downstream analysis, and can be re-computed identically if needed. - The many-to-one alignment file is not output anymore by default, to save
space. To keep this file, you can run the pipeline in
many-to-manymode with the--m2mparameter. - The
--seedparameter allows for all the existing values in thelastdbprogram. - Errors caused by absence of alignments at training or plotting steps are now ignored.
- New parameter
--export_aln_tothat creates additional files containing the alignments in a different format such as Axt, Chain, GFF or SAM.
Fixed
This release brings the pipeline to the standards of Nextflow 24.10.1 and nf-core 3.1.0. No changes were made to the alignment process.
Added a new softmask parameter, to optionally keep original softmasking.
Initial release. Thanks again to my colleagues, collaborators, and the nf-core community.
nf-core/pairgenomealign is a bioinformatics pipeline that aligns one or more query genomes to a target genome, and plots pairwise representations.
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