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Repository seq_primer_clip

Name: seq_primer_clip

Owner: peterjc

Synopsis: Trim off 5' or 3' primers

Detailed description:

Takes reads in FASTA, FASTQ or SFF format and looks for the given primer sequences
(within the existing clipped sequence) and further clips the reads to remove the
primers and any preceding/trailing sequence. Supports forward and reverse primers,
including IUPAC ambiguity codes.

Note this tool was initially written for Roche 454 data, and should also work fine
on Sanger or Ion Torrent as well. However, it is probably too slow for use on large
Illumina datasets.

Content homepage: https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip

Development repository: https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip

Link to this repository: https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip/0c79302b2c15

Clone this repository: hg clone https://testtoolshed.g2.bx.psu.edu/repos/peterjc/seq_primer_clip

Type: unrestricted

Revision: 23:0c79302b2c15

This revision can be installed: True

Times cloned / installed: 587

Tool dependencies - repository tools require handling of these dependencies
Name	Version	Type
biopython	1.67	package
galaxy_sequence_utils	1.0.1	package

Tool dependencies - repository tools require handling of these dependencies

Name

Version

Type

biopython

1.67

package

galaxy_sequence_utils

1.0.1

package

Valid tools - click the name to preview the tool and use the pop-up menu to inspect all metadata
Name	Description	Version	Minimum Galaxy Version
Primer clip sequences View tool metadata	Trim off 5' or 3' primers	0.0.16	16.01

Valid tools - click the name to preview the tool and use the pop-up menu to inspect all metadata

Name

Description

Version

Minimum Galaxy Version

View tool metadata

Trim off 5' or 3' primers

0.0.16

16.01