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Count how many sequencing reads (fastq) or contigs (fasta) contain each sequence of a reference fasta file, using Seal from BBTools.

seqcounter -ref refs.fasta -i samples/ -o results/

Reference   assembly  no_match  paired  single_end
absent      0         0         0       0
present     1         0         86      34
twice       1         0         154     65

Any set of short sequences works: spoligotype spacers, marker or resistance genes, primer or probe sequences, plasmid or phage fragments, barcodes, spike-ins. seqcounter does not interpret them; it counts them, the same way for reads and for assemblies, and writes the counts as a table, a per-sample summary and a JSON report.

Where to start

• Installation — conda, pip, or from a clone
• Tutorial — count IS6110 in three public samples, in ten minutes
• Usage — the input, every option, and what to expect
• Output files — the three reports, column by column
• How it works — what a count is, exactly, and how Seal is called
• Validation — the counts checked against known answers, in an assembly, in simulated reads and in public read sets
• Troubleshooting — when a count is 0, a sample fails, or Seal runs out of memory
• FAQ
• Changelog

What it is not

seqcounter reports counts; it does not call a genotype, a species or a presence/absence threshold. A count has to be read in the context of how much was sequenced, which the per-sample summary gives. Tools built on top of these counts decide what they mean: spoligotyper, for example, counts the 43 spacers of the direct repeat locus and reads them as a spoligotype.

Requirements

Python 3.10 or newer, and BBTools (seal.sh, which needs Java). seqcounter itself uses nothing but the Python standard library.

Citing

Please cite seqcounter and BBTools:

Duceppe M-O. seqcounter: count the occurrences of reference sequences in sequencing reads or genome assemblies. Zenodo. https://doi.org/10.5281/zenodo.23826933

That DOI resolves to the latest version. The "Cite this repository" button on the repository page gives the same citation in APA and BibTeX, from CITATION.cff.