The program sff-adaptersplitter utilizes source from sff2fastq written by Indraniel Das (indraniel@gmail.com or idas@wustl.edu) 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.
Given an SFF file, file.sff, and a barcode file, barcode.txt,you can simply run:
sff-adaptersplitter barcode.txt file.sff
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)>
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
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
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.
This software is provided "as is" without warranty of any kind.
August 9, 2012