Usage

Usage

See Installation for pip install brucetyper and the alternatives. Examples below use the installed brucetyper command; from a clone, python bruce_ladder.py takes exactly the same arguments.

# Every assay, on a folder of assemblies
brucetyper -i genomes/ -o results/

# One assay, on a single genome
brucetyper -i GCF_000054005.1.fna.gz -o results/ --amos

Input is a FASTA file or a folder of them, gzipped or not, one sample per file. Recognised extensions are .fasta, .fa, .fna, .fas, .seq and .ffn, each optionally .gz. The sample name is the file name with those extensions stripped. Assemblies, not reads.

--bruce, --suis, --amos and --rb51 select the assays; with none given, all four are run.

Option	Default	What it does
-t, --threads	all cores	FASTA files processed in parallel
--mismatches	2	Mismatches tolerated per primer
--three-prime	3	Bases at the 3' end of a primer that must match exactly
--tolerance	5	Size tolerance in bp when assigning an amplicon to an expected band
--min-size	50	Smallest product reported, primers included
--max-size	3000	Largest product reported, primers included

--tolerance has a ceiling, and it is well below the gap you might expect. It is bounded by the closest pair of band sizes in an assay: beyond half that gap the two windows overlap and a size in the overlap is assigned to the lower band, and beyond the gap itself the two bands merge. The closest pair is 120 bp for Bruce-ladder, 102 for AMOS and 463 for the RB51 junction assay, but only 21 bp for Suis-ladder, between its 278 and 299 bp bands — so --tolerance 11 already overlaps those two windows and 21 merges them. Raising it above 10 is not recommended; the measured cost of widening even a single band is on the Large scale validation page.

Output

Three kinds of report are written to --outdir:

• amplicons.tsv — every product found, with its locus, contig, strand, 1-based coordinates, size and the mismatch count of each primer.
• calls.tsv — one row per sample and assay: the call, the rough flag, the canonical bands that were present, the observed sizes, and any size belonging to no band of the assay.
• report_<assay>.tsv — sample and call, two columns, no header. This is the layout bruce_rates.py and suis_rates.py expect.

$ brucetyper -i genomes/ -o results/ --amos
Found 6 FASTA file(s)
Running in silico PCR for assay(s): amos
  RB51_or_2308: 3 amplicon(s)
  ...
Calling genotypes
Reports written to /path/to/results

$ cat results/calls.tsv
sample          assay  call             rough  bands         sizes         extra_bands
RB51_or_2308    amos   RB51_or_2308            178;387;494   494;387;178
S19             amos   S19                     494           494
abortus_bv1_2_4 amos   abortus_bv1_2_4         178;494       494;178
melitensis      amos   melitensis              178;733       733;178
ovis            amos   ovis                    178;976       976;178
suis_bv1        amos   suis_bv1                178;285       285;178

The rough column is empty above because only Bruce-ladder carries the band it reads.