Output Files

Final output of baits will be formatted as FASTA and named $out_baits.fasta (where $out is defined using the -o/–out flag). When the -t/–print_tr option is in use, targets will also be output as $out_targets.fasta, with an additional field in the header indicating if these targets passed or failed target selection and filtering.

By default, baits are reported with any ambiguity sequences included (e.g. as a consensus sequence) like so:

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>Locus1_Target4_Bait1
ATGTAATRAGGTATATG……
>Locus1_Target4_Bait2
TATGAATGTCGCGCGAT……
…
…
…

If using the -x/–expand option, ambiguities will be reported as all combinations, like so:

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>Locus2_Target4_Bait1.1
ATGTAATAAGGTATATG……
>Locus2_Target4_Bait1.1
ATGTAATGAGGTATATG……
>Locus1_Target4_Bait2.1
TATGAATGTCGCGCGAT……
…
…
…

Baits can also be printed as reverse complement. For example, if the –expand option was specified, in addition to –strand both:

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>Locus2_Target4_Bait1.1
ATGTAATAAGGTATATG……
>Locus2_Target4_Bait1.1_revcomp
TACATTATTCCATATAC……
>Locus2_Target4_Bait1.1
ATGTAATGAGGTATATG……
>Locus2_Target4_Bait1.1_revcomp
TACATTACTCCATATAC ……
>Locus1_Target4_Bait2.1
TATGAATGTCGCGCGAT……
>Locus1_Target4_Bait2.1_revcomp
ATACTTACAGCGCGCTA……
…
…

mrbait will also produce a .sqlite file (e.g. $out.sqlite) which can be used with the –resume flag to restart the pipeline at different stages- for example to re-perform bait filtering with different options. This stores the complete database, including all consensus loci parsed from the alignment input files, all targets, and all bait sequences (including those which failed filtering) and can be used independently with your own SQLite queries.