getRepresentativeAlignments: Import representative PacBio alignments.

In daewoooo/SaaRclust: R Package to cluster long sequencing reads into chromosomes to facilitate de novo genome assembly.

Description

This function selects the best representative PacBio alignements from multiple chunks in order to get the best estimates of theta values using Kmeans.

Usage

getRepresentativeAlignments(inputfolder = NULL, numAlignments = 30000,
  quantileSSreads = c(0.2, 0.8), minSSlibs = c(20, 25))

Arguments

inputfolder	A folder name where minimap files are stored.
numAlignments	A required number of representative PacBio alignments.
quantileSSreads	A quantile range for number of SSreads mapped to PB read. (default: 0.4-0.9)
minSSlibs	A range for the minimal and maximal number of StrandS libs being represented per PB read.

Value

A data.frame.

Author(s)

David Porubsky

daewoooo/SaaRclust documentation built on May 28, 2019, 7:50 p.m.