New --multi_cram option to produce a multi-query CRAM file combining all the alignments#114
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The merged CRAM file is neither a pangenome nor a multiple sequence alignment, but I find it very useful. Temporarly CRAM files are produced but not exported. Their header indicates only the name of the query genomes in the read group fields. The files are merged in a single CRAM file, where each read group represents one genome. Each target-query alignment is a one-to-one relationship so a base in the target is aligned at most once to each query. Care is taken to ensure that the path to the reference genome is relative to the current directory. The multi-query CRAM file is output in the same directory as its index and the BGZIpped genome, indexed too. Thus the multi-query CRAM file can be loaded and visualised in the IGV. The coverage plot shows how many query genomes align to the target at a given location. Expanded track view allows to visualise all the sequence differences. You can stabilise the order of the genomes, but IGV enforces alphanumeric sorting. You can work around this limitation by prefixing the sample IDs with numbers in the sample sheet. Custom scripts can (and have) be written to slice a pieces of the multi-query CRAM file and turn these pieces into real MSAs…
Will change to CRAM 3.1 in pairgenomealign 3.0.0.
Joon-Klaps
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Very minor things mostly on readabality.
Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be>
Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be>
Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be>
Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be>
Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be>
…which I submitted recently based on the local version.
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@Joon-Klaps Thanks to your comments I made big changes, can I ask you to have a look? |
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Main changes to the code:
samtools/mergemodule.Closes #60.
Details on the new feature:
The merged CRAM file is neither a pangenome nor a multiple sequence alignment, but I find it very useful.
Temporary CRAM files are produced but not exported. Their header indicates only the name of the query genomes in the read group fields.
The files are merged in a single CRAM file, where each read group represents one genome. Each target-query alignment is a one-to-one relationship so a base in the target is aligned at most once to each query.
Care is taken to ensure that the path to the reference genome is relative to the current directory. The multi-query CRAM file is output in the same directory as its index and the BGZIpped genome, indexed too.
Thus the multi-query CRAM file can be loaded and visualised in the IGV. The coverage plot shows how many query genomes align to the target at a given location. Expanded track view allows to visualise all the sequence differences.
You can stabilise the order of the genomes, but IGV enforces alphanumeric sorting. You can work around this limitation by prefixing the sample IDs with numbers in the sample sheet.
Custom scripts can (and have) be written to slice a pieces of the multi-query CRAM file and turn these pieces into real MSAs…
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).