compare genome assemblies using sequence similarity to transcript or protein sequences from a different species.
Perl
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
exoblast_test_files
MANIFEST
Makefile.PL
README.md
exoblast
gpl.txt

README.md

This repository is not being actively maintained

NOTE: I recommend BUSCO(http://busco.ezlab.org/) over exoblast for assessing assemblies

exoblast

DESCRIPTION

exoblast is being actively developed and tested. Please use with caution. I appreciate hearing about your experience with the program.

exoblast compares genome assemblies using sequence similarity to transcript or protein sequences from a different species.

INSTALLATION

To install this program and documentation type the following:

perl Makefile.PL
make
make install

RUN

exoblast --query=FASTA_FILE --blast=tblastn_OR_tblastx --out=PREFIX_FOR_OUTFILES --assembly=FASTA_ASSEMBLY1 --assembly=FASTA_ASSEMBLY2 [--assembly=ADDITIONAL_ASSEMBLY ...] [--num_queries=NUMBER_OF_QUERIES] [--eval=EVAL] [--threads=NUM_THREADS] [--blastdb=USE_EXISTING_BLASTDB] [--saveblastdb=PATH/FILE_TO_SAVE_GENERATED_BLASTDB] [--randomseed=RANDOMSEED_FOR_PICKING_QUERY_SEQS] [--min_contig_size=IGNORE_ASSEMBLED_SEQS_SHORTER_THAN_THIS] [--version] [--help]

TEST

exoblast --query=exoblast_test_files/prots.fa --assembly=exoblast_test_files/assembly1.fa --assembly=exoblast_test_files/assembly2.fa --blast=tblastn --out=test.exoblast

DOCUMENTATION

perldoc exoblast

DEPENDENCIES

This program requires Perl

It also requires BLAST+:

http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download

CITATION

Ryan, Joseph F., exoblast, (2014), GitHub repository, https://github.com/josephryan/exoblast

COPYRIGHT AND LICENSE

Copyright (C) 2014, 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/.