Difference between revisions of "Abacas"
(Created page with "=Introduction= algorithm-based automatic contiguation of assembled sequences = Basic usage = First, load the software module load abacas Then, make a folder with the refe...") |
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module load abacas | module load abacas | ||
| − | Then, make a folder with the reference | + | Then, make a folder with the reference sequence and a multifasta file with the contigs. |
When wanting to order contigs and design primers, the format of the commmand is: | When wanting to order contigs and design primers, the format of the commmand is: | ||
Revision as of 12:16, 7 June 2016
Introduction
algorithm-based automatic contiguation of assembled sequences
Basic usage
First, load the software
module load abacas
Then, make a folder with the reference sequence and a multifasta file with the contigs.
When wanting to order contigs and design primers, the format of the commmand is:
abacas -r <reference file: single fasta> -q <query sequence file: fasta> -p <nucmer/promer> [Options]
If ordering contigs is not required, this can be skipped so that primer design is the only task:
abacas.pl -r <reference file: single fasta> -q <pseudomolecule/ordered file: fasta> -e
In any case the following also gives help instructions:
abacas.pl -h
