TriageTools Wiki

TriageTools

TriageTools is a collection of tools for partitioning raw data from high-throughput sequencing projects. The tools are designed for basic data management as well for prioritizing analysis of certain subsets.

One of the more interesting tools in the collection is partitioning by sequence similarity with a target. This tool enables researchers interested in a small region (e.g. a couple of genes) to quickly extract from large fastq files those portions that are relevant to them. Using this tool in combination with fast aligners and variant callers, researchers working on exome or RNA-seq samples can obtain genotype information about the targeted regions in about an hour on a standard workstation.

The tools in the collection are:

• duplicates - split reads into unique and duplicate sequences
• parts - split into parts at random
• length - partition by read length
• lzw - partition by sequence complexity (LZW-based)
• quality - partition by median base quality score
• readid - extract reads using ids
• regex - partition using regular expression pattern matching
• sequence - partition according to similarity with a target sequence

Additional resources:

• common options - many of the tools share some common options.
• version history - overview of changes and improvements

Download

The default download contains object-code, source-code, and all third-party libraries.

References

D. Fimereli, V. Detours, T. Konopka. TriageTools: tools for partitioning and prioritizing analysis of high-throughput sequencing data. Nucleic Acids Research 2013.