DeconSeq

Application data
Created by	Robert Schmieder
Biological application domain(s)	Transcriptomics, Metagenomics, Genomics
Principal bioinformatics method(s)	Sequence contamination filtering
Technology	Sanger, 454, Ion Torrent, PacBio
Created at	San Diego State University, Sourceforge
Maintained?	Yes
Input format(s)	FASTA, FASTQ, (Compressed) FASTA, (Compressed) FASTQ
Output format(s)	FASTA, FASTQ
Programming language(s)	Perl, C
Licence	GPLv3
Operating system(s)	UNIX, Mac OS X

Summary: DeconSeq can be used to automatically detect and efficiently remove any type of sequence contamination from metagenomic datasets, including human or other host sequences. The tool uses a modified version of the BWA-SW aligner and can be applied to longer-read datasets (150+bp read length). DeconSeq is available as both standalone and web-based versions.

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Description

Sequences obtained from impure nucleic acid preparations may contain DNA from sources other than the sample. Those sequence contaminations are a serious concern to the quality of the data used for downstream analysis, possibly causing misassembly of sequence contigs and erroneous conclusions. Therefore, the removal of sequence contaminants presents a necessary step for all metagenomic projects.

There are several advantages in using DeconSeq to pre-process sequence data: (i) Removal of potential sequence contaminations improve the reliability of downstream data analysis (ii) The web application that allows users to pre-process their datasets without installing any software (iii) It takes about 10-15 minutes to screen an average size metagenome for human contamination