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
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
isoblat [--version] [--help] [--max_gap_to_consider_missing=INT] [--min_to_count_as_coverage=INT] BLAT_FILE FASTA_QUERY_USED_IN_BLAT
This program requires Perl
You will also want BLAT:
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/.