ssiamb

ssiamb counts ambiguous SNV sites from trimmed paired-end reads mapped back to their own assembly.

The first supported workflow matches production use at SSI:

ssiamb self \
    --r1 reads_R1.fastq.gz \
    --r2 reads_R2.fastq.gz \
    --assembly shovill_assembly.fasta \
    --sample SAMPLE \
    --outdir outputs

The tool assumes reads are already trimmed and the assembly has already been created, for example by Shovill.

Method

The default flow maps reads to the supplied assembly with minimap2, sorts the alignment with samtools, calls variants with BBTools callvariants.sh, then groups VCF records by (CHROM, POS) before counting ambiguous loci.

Default ambiguity criteria:

• DP >= 10
• MAF >= 0.10
• same-position ALT allele frequencies are summed before converting to MAF
• high ALT frequencies are converted with MAF = min(AF, 1 - AF)
• filtered caller records remain visible in diagnostics and are not hidden from the primary candidate set

Outputs

For sample SAMPLE, the CLI writes:

• SAMPLE.summary.tsv: one-row summary
• SAMPLE.loci.tsv: grouped locus diagnostics
• SAMPLE.matrix.tsv: cumulative depth/MAF matrix
• SAMPLE.variants.vcf: raw called variants
• SAMPLE.provenance.json: command, thresholds, inputs, outputs, and tool info

External Tools

The end-to-end self workflow requires these commands on PATH:

• minimap2
• samtools
• callvariants.sh from BBTools/BBMap

Core VCF grouping and counting logic is pure Python and covered by unit tests.