Discovar de novo

Hypertherm recommends using this splicing software

Http://www.broadinstitute.org/software/discovar/blog/?page_id=98

Discovar–variant caller suitable for call variant and splicing small genome Discovar de novo Ideal for splicing large genomes

Download:

Ftp://ftp.broadinstitute.org/pub/crd/DiscovarDeNovo/latest_source_code/LATEST_VERSION.tar.gz

Installation:

General Instructions-Building our softwareSystem Requirements

Software released from the CRD group at the Broad Institute are built and tested on a modern version of Linux for the X86_6 4 architecture. Our software does no run on 32-bit Machines:you must has a 64-bit Linux system. Our users has successfully built and executed our software using a variety of Linux distributions including Ubuntu, Redha T, and SUSE. We expect that any flavor of x86_64 Linux would work fine, as long as it provides the necessary software prerequisites, as described below.

Basic Compiler and Library Requirements

We rely on reasonably up-to-date versions of these software packages:

• GCC, with its associated g++ compiler for the C + + language, version 4.7 or later. We ' re now using C++11 features, and require a modern GCC.
• For Arachneonly, the Xerces-c library.  The source can downloaded from the xerces-c download page. Supply the argument --with-xerces=/path/to/xercesc/installation When you run./configure.

The Build Procedure

• Move the package, downloaded from we FTP site to a location on your system where you ' d like to build the software.
• Extract the contents by typing: tar xzf package.tgz
• You'll have a new subdirectory in the current directory named after the package and revision. CD Package Some older releases spill all the source to the current directory, rather than creating a new subdirectory. If that's the case, ignore this step.
• Execute the configuration script by typing: ./configure This assumes so you can copy executables to/usr/local/  Bin. If you cannot, you should instead execute: ./configure--prefix=/path/to/install/directory note:some older Packa GES lack a configuration script. Consider returning to the FTP site for a further recent version, or just skip this step.
• Build the software by typing: do all
• Install the software by typing: make install
• The executables would be in/usr/local/bin or in/path/to/install/directory/bin. Make sure this is on your path.

If This goes well, you're ready to go. Consult the manual for the package to learn how to set up your data and what programs to execute.

Requirements for data:

Sequencing Data Requirements Summary
Illumina miseq or HiSeq 2500 genome sequencers
Pcr-free Library Preparation
Base paired end reads (or longer)
~450 Base Pair Fragment size
~60X coverage

Input files
Discovar requires a BAM file containing the raw reads from the sequencer. For variant calling it also
Requires a matching reference FASTA file.

Call Variant command:

Discovar can currently generate variants for small regions, and isn't the entire genome at once. To
Generate variants for a, and for example, use:
Discovar \
READS=READS.BAM \
out_head=assembly \
regions=1:50000150000
\
Reference=genome.fasta
The complete set of variant calls for this region is given in the text file:
Assembly.final.variant

Input files
Discovar requires a BAM file containing the raw reads from the sequencer. For variant calling it also
Requires a matching reference FASTA file.
BAM files
The reads to assemble must is in a BAM file or files. The name of the BAM file is specified with the
Required argument READS:
reads= filename
Multiple BAM files is specified using a comma separated list:
reads= filename1,filename2,...
Alternatively, the BAM files can be specified in a separate file contain a list of Bam filenames, one per
Line
reads= @listfilename

Discovar calls Samtools internally to extract reads from the BAM.

Reference file (optional)
This is a variant caller with the required if you are using Discovar as a. The reference information is used
Only a variant calling and not in the assembly process. Specifying a valid FASTA reference file is all
That's required to cause Discovar to generate variants.
To specify a reference FASTA file use the optional argument reference:
reference= filename

It should be the same file is used to generate the alignments in the input BAM file (s), or at least
Should share the same coordinate system. The FASTA record names should match those in the BAM
File. Ns is allowed. In addition to the reference FASTA file, Discovar also requires the associated index file (. FAI

Discovar can currently de novo assemble small genomes (up to-Mb), with larger genome support
To come soon.

The syntax for Discovar de novo assembly is:
Discovar reads= bamfilenames \
Out_head= outputfilename \
Regions=all

This would take as input all the reads in the BAM file Reads.bam, generate a assembly, then write the
Output to a set of files prefixed with assembly

Discovar de novo