SCRIPT

Cite as: Jennifer Shelton and Zachary Sliefert (2015). BNGCompare: BNGCompare.pl Version 1.1. Zenodo. 10.5281/zenodo.17586

BNGCompare.pl - Script outputs summary stats from a FASTA and an in silico CMAP (reference) of the same FASTA and a of a CMAP inferred from assembly of BioNano molecule maps (query) as well as a summary of an XMAP generated aligning the CMAPs.

USAGE

perl BNGCompare.pl [options]

Documentation options:

-help    brief help message
-man            full documentation

Required parameters:

-f      genome FASTA
-q      CMAP inferred from assembly of BioNano molecule maps (query)
-r      in silico CMAP (reference)
-x      XMAP generated aligning the CMAP

Optional parameters:

-o      output filename

Options:

-help   Print a brief help message and exits.

-man    Prints the more detailed manual page with output details and
examples and exits.

-f, --input_fasta
The fullpath for the genome FASTA file.

-r, --ref
The fullpath for the in silico CMAP (reference) of the genome
FASTA.

-q, --que
The fullpath for the CMAP inferred from assembly of BioNano
molecule maps (query).

-x, --xmap
The fullpath for the XMAP generated by aligning the reference
and query CMAPs.

-o, --out
The fullpath for the in output comma separated values file.

DESCRIPTION

OUTPUT DETAILS:

Script outputs a CSV file with the file prefix "BNGCompare.csv" that includes
summary metrics for XMAP alignment's query map (e.g. where "total aligned
length" is the length of the aligned region for the query in silico genome
maps), the genome FASTA, in silico CMAP, and the in silico CMAP from FASTA file.

UPDATES

####BNGCompare.pl Version 1.1

Added optional -o output filename parameter