linkChunks: Link pattern-matches on contig/genome chunks

In ProActive: Detect Elevations and Gaps in Mapped Sequencing Read Coverage

Link pattern-matches on contig/genome chunks

Description

Detect partial gap/elevation pattern matches that fall on the edges of chunked genomes/contigs that may be part of the same pattern prior to chunking

Usage

linkChunks(bestMatchList, pileup, windowSize, mode, verbose)

Arguments

bestMatchList	A list containing pattern-match information associated with all contigs/chunks classified by 'ProActive()' pattern-matching
pileup	A .txt file containing mapped sequencing read coverages averaged over 100 bp windows/bins.
windowSize	The number of basepairs to average read coverage values over.
mode	Either "genome" or "metagenome"
verbose	TRUE or FALSE. Print progress messages to console. Default is TRUE.

ProActive documentation built on April 4, 2025, 12:58 a.m.