mlgt Works through all pairs of markers and
samples. Aligns variants and trims aligned variants to
the marker sequence. Potential 'alleles' are assigned
from the most common variants within each sample.
mlgt(designObject, maxVarsToAlign = 30, minTotalCount = 500, errorCorrect = FALSE, correctThreshold = 0.01, minLength = 70)mlgtDesignmlgtResult containing
all variants and their counts, a summary table (all
markers) and one summary table per marker.
prepareMlgtRun having been run
in the current directory to generate
designObject of class mlgtDesign.
The basic process for each marker/sample pair is to align
all unique variants using MUSCLE and then extract the
alignment portion aligned to the reference marker
sequence, ignoring the rest. The marker alignment is
critical and mlgt has several options to
optimise this alignment. If the total number of reads is
less than minTotalCount, then all variants are aligned.
Otherwise, only the most abundant 30 unique variants are
aligned. Optionally, alignments are `error-correted' as
per the separate function errorCorrect.
Reads shorter than 'minLength' are filtered out.
prepareMlgtRun