use RNA transcripts to assess assembly - this program parses the output of a BLAT run of transcriptome vs. a genome. It returns 1) Total % mapped, 2) average %coverage of a mapping, and 3) number of transcripts mapping to a single contig/scaffold. It is simple to run. Just run the blat (transcripts vs. genome) and then run the script with the bl…
Perl
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MANIFEST
Makefile.PL
README.md
TODO
gpl.txt
isoblat

README.md

isoblat

use RNA transcripts to assess assembly - parses BLAT output of transcriptome vs. genome

The output looks something like:

Percentage of transcripts with a BLAT entry (15661/15752): 0.994222955815135
Total % coverage of all positions (10303278 / 10491059): 0.982100853688841
Number of transcripts mapping to a single contig/scaffold: (14750/15661) 0.941830023625567
Average number of contigs/scaffolds per mapped transcript: 1.08715918523721

INSTALLATION

To install this program and documentation type the following:

perl Makefile.PL
make
make install

To install without root privelages try:

perl Makefile.PL PREFIX=/home/myuser/scripts
make
make install

RUN

isoblat [--version] [--help] [--max_gap_to_consider_missing=INT] [--min_to_count_as_coverage=INT] [--pblat] BLAT_FILE FASTA_QUERY_USED_IN_BLAT

DOCUMENTATION

perldoc isoblat

DEPENDENCIES

This program requires Perl

You will also want BLAT:

http://users.soe.ucsc.edu/~kent/src/

CITATION

Ryan, Joseph F. "Baa. pl: A tool to evaluate de novo genome assemblies with RNA transcripts."
    arXiv preprint arXiv:1309.2087 (2013).

COPYRIGHT AND LICENSE

Copyright (C) 2012,2013 Joseph F. Ryan

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program in the file gpl.txt. If not, see http://www.gnu.org/licenses/.