NAME

novo_wrapper.pl

A parallelized wrapper program for Novocraft's novoaligner.

SYNOPSIS

novo_wrapper.pl --index <file> [--options] <seq_file1> ...
 
 Options:
 --in <seq_file>
 --index </path/to/novoalign_index>
 --repeat [None | All | Random | Exhaustive]
 --split
 --cores <integer>
 --opt <"text">
 --novo </path/to/novoalign>
 --sam </path/to/samtools>
 --version
 --help

OPTIONS

The command line flags and descriptions:

--in <seq_file>

Specify the name(s) of the input Fastq sequence files. Multiple files may be specified using multiple --in arguments, with a single --in argument and a comma delimited list, or as a list at the end of all options. The files may kept gzipped; they will automatically be uncompressed.

--index <novo_index>

Specify the path to genome database index file to which the sequences will be aligned. The file should be built using Novocraft's 'novoindex' program.

--repeat [None | All | Random | Exhaustive]

Specify the novoalign option of dealing with sequences which align to multiple locations in the genome (repeats). See the Novoalign documentation for more information. Default value is None.

--split

Indicate that the input file should be split into numerous files (2 million lines each) and multiple instances of Novoalign should be executed. This requires the GNU 'parallel' utility to be installed.

--cores <integer>

When used with the --split option, this will limit the number of Novoalign instances executed at once. Default is 4.

When using a paid, licensed version of Novoalign, skip the --split option and specify as many CPU cores you want Novoalign to use in multi-threaded execution. Default is 1 (assume free academic version of Novoalign).

--opt <"text">

Specify any additional options you want to passed to the Novoalign executable. See the documentation for Novoalign for a full list of available options. Must enclose in quotes.

--novo </path/to/novoalign>

Optionally specify the full path to Novocraft's 'novoalign' executable file. It may also be specified in the 'biotoolbox.cfg' file, or it may be automatically identified by searching the environment path.

--sam </path/to/samtools>

Optionally specify the full path to the 'samtools' executable file. It may also be specified in the 'biotoolbox.cfg' file, or it may be automatically identified by searching the environment path.

--version

Print the program version number.

--help

This help text.

DESCRIPTION

This program is a wrapper for Novocraft's Novoalign alignment tool. It also performs a number of post-alignment functions, including converting the alignments into a sorted, indexed, Bam file using samtools.

When using the unlicensed, free, academic version of Novoalign that is limited to single-thread execution, novo_wrapper.pl can split the input file into numerous smaller versions and execute multiple instances of Novoalign. This requires the Parallel::ForkManager module for managing multiple executions. Note that only a limited number of instances should be run simultaneously; too many and your system may come to a standstill.

Licensed versions of Novoalign are multi-threaded and do not need to be split.

Novoalign is executed with the "-s 2", and "-r None" as default options. Additional custom options may be passed on to Novoalign by using the --opt flag above.

AUTHOR

Timothy J. Parnell, PhD
Howard Hughes Medical Institute
Dept of Oncological Sciences
Huntsman Cancer Institute
University of Utah
Salt Lake City, UT, 84112

This package is free software; you can redistribute it and/or modify it under the terms of the GPL (either version 1, or at your option, any later version) or the Artistic License 2.0.