nf-core pipeline · comparative-genomics, dot-plot, genomics
nf-core/pairgenomealign
Pairwise whole-genome alignment of query genomes against a target genome using the LAST toolchain.
What nf-core/pairgenomealign is
nf-core/pairgenomealign is a bioinformatics workflow designed to conduct pairwise whole-genome alignments between one or more query genomes and a target reference genome. Originally developed by Charles Plessy and maintained within the nf-core community, it coordinates the tools of the LAST suite into a structured, reproducible pipeline.
Pairwise genome comparison is central to assessing sequence conservation, structural rearrangements, and evolutionary divergence. By incorporating adaptive seeding, automated parameter training, and global-score optimisation (chaining), the pipeline allows researchers to compare both closely related and divergent assemblies while balancing sensitivity, runtime, and memory.
What the pipeline does
The workflow first assesses input genome quality using assembly-scan before indexing the target assembly with lastdb. Target indexing seeding parameters can be adjusted to balance sensitivity against processing time and memory consumption. Next, last-train deduces empirical alignment scoring parameters directly from the sequence data. Pairwise alignments are then performed using lastal via adaptive seeding and chaining.
Following alignment, last-split can be applied to reduce the results to a best global one-to-one relationship. Pairwise visualisations are generated as dot plots using last-dotplot. Finally, maf-convert and Samtools convert alignment outputs from MAF format into coordinate-only formats (PSL, GFF) or standard sequence alignment files (SAM, BAM, and CRAM).
Key facts
- Core tools
- assembly-scan, LAST (lastdb, last-train, lastal, last-split, last-dotplot, maf-convert), Samtools
- Pipeline framework
- Nextflow (nf-core)
- Input formats
- FASTA (target assembly and query assemblies via CSV samplesheet)
- Output formats
- MAF, PSL, GFF, SAM, BAM, CRAM, and dot plots
- Latest release
- 3.0.4
- Original author
- Charles Plessy
What you can use it for
- Synteny analysis
- Identify conserved collinear gene blocks and chromosomal rearrangements across genomes by filtering alignments to a best global one-to-one set with last-split.
- Duplication and repeat exploration
- Analyse internal duplications and repetitive sequences across assemblies by generating unfiltered pairwise or self-alignments.
- Cross-species comparative genomics
- Align divergent or closely related assemblies by using last-train to discover scoring parameters automatically without manual tuning.
- Rapid visual inspection
- Produce dot-plot visualisations to quickly assess large-scale structural variations, inversions, and translocations between query and target assemblies.
Run it here
The research agent runs nf-core/pairgenomealign with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
Strengths and limits
Good at
- Infers scoring parameters automatically with last-train, eliminating the need to tune alignment scoring manually.
- Supports both unfiltered output for repeat detection and one-to-one filtering for synteny analysis.
- Converts alignment outputs into coordinate-only (PSL, GFF) and standard alignment formats (MAF, SAM, BAM, CRAM).
- Handles both closely related and divergent genomes through adjustable seeding trade-offs in lastdb.
Watch out for
- Custom configuration files cannot be used to pass pipeline parameters, which must instead be provided via CLI options or parameter files.
- Performs pairwise alignments against a single target genome rather than progressive or simultaneous multiple-genome alignments.
Questions
Can I run nf-core/pairgenomealign without my own cluster?
The research agent runs nf-core/pairgenomealign with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
What licence is nf-core/pairgenomealign under?
MIT, like every nf-core pipeline.
What input data does the workflow accept?
It requires a target sequence in FASTA format provided via the target parameter, alongside a CSV samplesheet listing sample identifiers and FASTA file paths for one or more query genomes.
How does the pipeline accommodate divergent genomes?
Users can adjust target index seeding parameters to enhance alignment sensitivity for distantly related assemblies, while last-train estimates custom scoring matrices directly from the input sequences.
What visual outputs are generated?
The pipeline generates dot-plot visualisations using last-dotplot to allow rapid graphical inspection of pairwise alignments.
Can alignments be filtered to remove many-to-many matches?
Yes. The pipeline uses last-split to reduce pairwise alignments to a best global one-to-one set for synteny investigation.
How to cite it
Charles Plessy, Michael J. Mansfield, Aleksandra Bliznina, Aki Masunaga, Charlotte West, Yongkai Tan, Andrew W. Liu, Jan Grašič, María Sara del Río Pisula, Gaspar Sánchez-Serna, Marc Fabrega-Torrus, Alfonso Ferrández-Roldán, Vittoria Roncalli, Pavla Navratilova, Eric M. Thompson, Takeshi Onuma, Hiroki Nishida, Cristian Cañestro, Nicholas M. Luscombe. Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species. Genome Res. 2024. 34: 426-440; doi: 10.1101/2023.05.09.539028. PubMed ID: 38621828
Written from nf-core/pairgenomealign's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.