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Repository trtr
Name: trtr
Owner: mrvollger
Synopsis: TRTR Trim Reads of Tandem Repeats. Recommended before calling SNPs.
This tool removes tandem repeats from ends of unaligned sequencing reads (leaving one copy). This prevents reads that don't span the repeated region from overlapping, leading to innaccurate SNPs calls.

The maximimum repeat length is adjustable (use 1 to trim only homopolymers).

The "aggressive" option should not be touched in general. Setting to 0 will prevent the program from trimming to exactly 1 copy of the repeat, instead leaving between 1 and 2 copies.

This could also be a useful first step before assembly. More testing needs to be done.
Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/mrvollger/trtr
Type: unrestricted
Revision: 32:3adf1893cb04
This revision can be installed: True
Times cloned / installed: 475
Dependencies of this repository

Repository package_trtr_0_1 revision ada63ad7c4d2 owned by mrvollger

Name Version Type
trtr 1.0 package

Contents of this repository

Name Description Version Minimum Galaxy Version
Trim Reads of Tandem Repeat in a fastq file. 1.0galaxy1 any

Categories
Fastq Manipulation - Tools for manipulating fastq data
Sequence Analysis - Tools for performing Protein and DNA/RNA analysis
Text Manipulation - Tools for manipulating data
Variant Analysis - Tools for single nucleotide polymorphism data such as WGA