This is the command abacas that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
abacas - Algorithm Based Automatic Contiguation of Assembled Sequences
SYNOPSIS
abacas -r ref -q qs -p prog [OPTIONS]
OR
abacas -r ref -q psf -e
ref reference sequence in a single fasta file
qs contigs in multi-fasta format
rog MUMmer program to use: 'nucmer' or 'promer'
psf pseudomolecule/ordered sequence file in fasta format
OPTIONS
-h print usage
-d use default nucmer/promer parameters
-s int minimum length of exact matching word (nucmer default = 12, promer default
= 4)
-m print ordered contigs to file in multifasta format
-b print contigs in bin to file
-N print a pseudomolecule without "N"s
-i int mimimum percent identity [default 40]
-v int mimimum contig coverage [default 40]
-V int minimum contig coverage difference [default 1]
-l int minimum contig length [default 1]
-t run tblastx on contigs that are not mapped
-g string (file name) print uncovered regions (gaps) on reference to file name
-a append contigs in bin to the pseudomolecule
-o prefix output files will have this prefix
-P pick primer sets to close gaps
-f int number of flanking bases on either side of a gap for primer design (default
350)
-R int Run mummer [default 1, use -R 0 to avoid running mummer]
-e Escape contig ordering i.e. go to primer design
-c Reference sequence is circular
DESCRIPTION
ABACAS is intended to rapidly contiguate (align, order, orientate), visualize and design
primers to close gaps on shotgun assembled contigs based on a reference sequence.
ABACAS uses MUMmer to find alignment positions and identify syntenies of assembled contigs
against the reference. The output is then processed to generate a pseudomolecule taking
overlapping contigs and gaps in to account. ABACAS generates a comparision file that can
be used to visualize ordered and oriented contigs in ACT. Synteny is represented by red
bars where colour intensity decreases with lower values of percent identity between
comparable blocks. Information on contigs such as the orientation, percent identity,
coverage and overlap with other contigs can also be visualized by loading the outputted
feature file on ACT.
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