https://github.com/blahah/idba_tran

Mirror of IDBA tran to provide a stable location for binary distribution
https://github.com/blahah/idba_tran

Last synced: 6 days ago
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Mirror of IDBA tran to provide a stable location for binary distribution

• Host: GitHub
• URL: https://github.com/blahah/idba_tran
• Owner: blahah
• Created: 2015-05-22T11:52:32.000Z (over 9 years ago)
• Default Branch: master
• Last Pushed: 2015-05-22T12:19:09.000Z (over 9 years ago)
• Last Synced: 2024-04-16T01:01:02.880Z (7 months ago)
• Language: C++
• Size: 336 KB
• Stars: 0
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README
  • Changelog: ChangeLog

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README

        
###############################################################################

Copyright (C) 2009 Yu Peng ([email protected])

This program is free software; you can redistribute it and/or

modify it under the terms of the GNU General Public License

as published by the Free Software Foundation; either version 2

of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful,

but WITHOUT ANY WARRANTY; without even the implied warranty of

MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

GNU General Public License for more details.

You should have received a copy of the GNU General Public License

along with this program; if not, write to the Free Software

Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.

Yu Peng ([email protected])

Dept. of Computer Science,

The University of Hong Kong,

Pokfulam Road,

Hong Kong,

China

###############################################################################

Requirement

This software is suitable for all unix-like system with gcc installed.

Installation Guide

Exract the package, then use make to compile the source code.

$ ./configure

$ make

Introduction

IDBA is the basic iterative de Bruijn graph assembler for second-generation sequencing reads. 

IDBA-UD, an extension of IDBA, is designed to utilize paired-end reads to assemble low-depth 

regions and use progressive depth on contigs to reduce errors in high-depth regions. It is a 

generic purpose assembler and epspacially good for single-cell and metagenomic sequencing data. 

IDBA-Hybrid is another update version of IDBA-UD, which can make use of a similar reference 

genome to improve assembly result. IDBA-Tran is an iterative de Bruijn graph assembler for 

RNA-Seq data.

The basic IDBA is included for comparison, you should use more specific assemblers for your data.

If you are assembling genomic data without reference, please use IDBA-UD.

If you are assembling genomic data with a similar reference genome, please use IDBA-Hybrid.

If you are assembling transcriptome data, please use IDBA-Tran.

Comments

Note that IDBA assemblers are designed for short reads (around 100bp). If you want to assemble 

paired-end reads with longer read length, please modify the constant kMaxShortSequence in 

src/sequence/short_sequence.h to support longer read length.

Please find the manual by running the assembler without any parameters. For example:

$ bin/idba

IDBA series assemblers accept fasta format reads. Fastq format reads can be converted by 

fq2fa program in the packcage.

$ bin/fq2fa read.fq read.fa

IDBA-UD IDBA-Hybrid and IDBA-Tran require paired-end reads stored in single FastA file and a pair of

reads is in consecutive two lines. If not, please use fq2fa to merge two

FastQ read files to single file.

$ bin/fq2fa --merge --filter read_1.fq read_2.fq read.fa

or convert a FastQ read file to FastA file.

$ bin/fq2fa --paired --filter read.fq read.fa

The this tools assume the paired-end reads are in order (->, <-). If your data is in order (<-, ->), 

please convert it by yourself.