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Demultiplex 454 Genome Sequencer reads from a SFF file

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SYNOPSIS

The program sff-adaptersplitter utilizes source from sff2fastq written by Indraniel Das ([email protected] or [email protected]) from The Genome Institute at Washington University, St. Louis, MO.

It takes a multiplexed SFF file, produced by the 454 genome sequencer, and demultiplexes the reads according to given barcodes into separate SFF files per adapter.

USAGE

Given an SFF file, file.sff, and a barcode file, barcode.txt,you can simply run:

sff-adaptersplitter barcode.txt file.sff

Options

sff-adaptersplitter can search for adapters on the entire read sequence or only using the quality trimmed sequence. Trimming is turned on by default, but can be turned off like this:

sff-adaptersplitter barcode.txt file.sff <trimming 0|1 (default: 1)>

Barcode files

The barcode files supplied to sff-adaptersplitter are simple tab-separated text files with barcode-ID in the first column and barcode-sequence in the second column, e.g.

IonXpress_001	CTAAGGTAAC
IonXpress_002	TAAGGAGAAC
IonXpress_003	AAGAGGATTC

INSTALLATION

In order to build sff-adaptersplitter only cmake (>=2.8) and g++ are required. Typically these tools should be already available on your computer. If not, please install them. The installation process utilizes cmake to create a simple Makefile, which can then build with standard make.

mkdir build
cd build
cmake ..
make
../bin/sffsplit

NOTES

This has been successfully compiled on Linux/Ubuntu 14.04 LTS and Linux/Ubuntu CentOS 7 workstations (64-bit machines), and on Mac OS X (10.11). Compiling on other types of operating systems and architectures has not been experimented upon.

AUTHORS

Tobias Neumann

DISCLAIMER

This software is provided "as is" without warranty of any kind.

August 9, 2012

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  • C++ 61.3%
  • C 37.6%
  • CMake 1.1%