build_contigs: build_contigs

In mskilab/loosends: Classifying loose ends in gGraphs

build_contigs

Description

Assemble reads surrounding seed window supplied in seed.frame column of data table Performs alignment for a max number of iterations or until all reads are aligned

Usage

build_contigs(
  reads.dt,
  col = "seed.frame",
  qcol = "qual",
  max.iter = 3,
  max.unaln = 3,
  verbose = FALSE
)

Arguments

reads.dt	(must have column seed.frame)
col	(column name containing sequences for alignment) e.g. seed.frame
qcol	(column name for base quality, default 'qual')
max.iter	(numeric) max number of iterations for assembly
max.unaln	(numeric) max number of unaligned reads after assembly
verbose	(logical) default FALSE

mskilab/loosends documentation built on Aug. 24, 2023, 8:08 a.m.