abacas(1) [debian man page]
ABACAS(1) User Commands ABACAS(1) 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 pro- cessed 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. AUTHOR
ABACAS IS Copyright (C) 2008-10 The Wellcome Trust Sanger Institute, Cambridge, UK. This manual page was written by Andreas Tille <tille@debian.org>, for the Debian project (and may be used by others). 1.3.1 2011-02-11 ABACAS(1)
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Bio::Assembly::ScaffoldI(3pm) User Contributed Perl Documentation Bio::Assembly::ScaffoldI(3pm) NAME
Bio::Assembly::ScaffoldI - Abstract Inteface of Sequence Assemblies SYNOPSIS
# get a Bio::Assembly::ScaffoldI object somehow foreach my $contig ($assembly->all_contigs) { # do something (see Bio::Assembly::Contig) } DESCRIPTION
This interface defines the basic set of methods an object should have to manipulate assembly data. FEEDBACK
Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists Support Please direct usage questions or support issues to the mailing list: bioperl-l@bioperl.org rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - Robson Francisco de Souza Email: rfsouza@citri.iq.usp.br APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ Accessing general assembly data get_nof_contigs Title : get_nof_contigs Usage : $assembly->get_nof_contigs() Function: Get the number of contigs included in the assembly Returns : integer Args : none get_nof_singlets Title : get_nof_singlets Usage : $assembly->get_nof_singlets() Function: Get the number of singlets included in the assembly Returns : integer Args : none get_contig_ids Title : get_contig_ids Usage : $assembly->get_contig_ids() Function: Access list of contig IDs from assembly Returns : an array if there are any contigs in the assembly. undef otherwise Args : an array of contig IDs get_singlet_ids Title : get_singlet_ids Usage : $assembly->get_singlet_ids() Function: Access list of singlet IDs from assembly Returns : an array if there are any singlets in the assembly. undef otherwise Args : an array of singlet IDs get_contig_by_id Title : get_contig_by_id Usage : $assembly->get_contig_by_id($id) Function: Get a reference for a contig from the assembly Returns : a Bio::Assembly::Contig object or undef Args : [string] contig unique identifier (ID) get_singlet_by_id Title : get_singlet_by_id Usage : $assembly->get_singlet_by_id() Function: Get a reference for a singlet from the assembly Returns : Bio::Assembly::Singlet object or undef Args : [string] a singlet ID Modifier methods Implementation of these methods is optional in the sense that read-only implementations may not have these. If an object implements one of them, it should however implement all. add_contig Title : add_contig Usage : $assembly->add_contig($contig) Function: Add another contig to the Bio::Assembly::ScaffoldI object Returns : 1 on success, 0 otherwise Args : a Bio::Assembly:Contig object See Bio::Assembly::Contig for more information add_singlet Title : add_singlet Usage : $assembly->add_singlet($seq) Function: Add another singlet to the Bio::Assembly::ScaffoldI object Returns : 1 on success, 0 otherwise Args : a Bio::Assembly::Singlet object remove_contigs Title : remove_contigs Usage : $assembly->remove_contigs(1..4) Function: Remove contig from assembly object Returns : a Bio::Assembly::Contig object Args : a list of contig IDs See function get_contig_ids() above remove_singlets Title : remove_singlets Usage : $assembly->remove_singlets(1..4) Function: Remove singlets from assembly object Returns : an array of Bio::Assembly::Singlet objects Args : an array of singlet IDs See function get_singlet_ids() above Contig and singlet selection methos select_contigs Title : select_contig Usage : $assembly->select_contig Function: Selects an array of contigs from the assembly Returns : an array of Bio::Assembly::Contig objects Args : an array of contig ids See function get_contig_ids() above select_singlets Title : select_singlets Usage : $assembly->select_singlets(@list) Function: Selects an array of singlets from the assembly Returns : an array of Bio::Assembly::Singlet objects Args : an array of singlet ids See function get_singlet_ids() above all_contigs Title : all_contigs Usage : my @contigs = $assembly->all_contigs Function: Returns a list of all contigs in this assembly. Contigs are both clusters and alignments of one or more reads, with an associated consensus sequence. Returns : array of Bio::Assembly::Contig Args : none all_singlets Title : all_singlets Usage : my @singlets = $assembly->all_singlets Function: Returns a list of all singlets in this assembly. Singlets are isolated reads, without non-vector matches to any other read in the assembly. Returns : array of Bio::Assembly::Singlet objects Args : none perl v5.14.2 2012-03-02 Bio::Assembly::ScaffoldI(3pm)