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Repository seq_primer_clip
Owner: peterjc
Synopsis: Trim off 5' or 3' primers
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.
Type: unrestricted
Revision: 23:0c79302b2c15
This revision can be installed: True
Times cloned / installed: 504
Dependencies of this repository

Repository package_numpy_1_9 revision 1e2b7e63dec2 owned by iuc (prior install required)
Repository package_atlas_3_10 revision 35d6b30ef137 owned by iuc (prior install required)
Repository package_python_2_7 revision a03693de8e0c owned by iuc (prior install required)
Repository package_zlib_1_2_8 revision 3348f1acee2a owned by iuc (prior install required)
Repository package_readline_6_3 revision de22495ddf2b owned by iuc (prior install required)
Repository package_bzlib_1_0 revision 29f79feefc77 owned by iuc (prior install required)
Repository package_xz_5_0_5 revision c9d30f1de10a owned by iuc (prior install required)
Repository package_sqlite_3_8_3 revision 9ba893c2353f owned by iuc (prior install required)
Repository package_gdbm_1_11 revision 77ea468f199e owned by iuc (prior install required)
Repository package_ncurses_6_0 revision 15e2190c87ca owned by iuc (prior install required)
Repository package_ncurses_6_0 revision 15e2190c87ca owned by iuc (prior install required)
Repository package_libtool_2_4 revision 5ccfb33b5622 owned by iuc (prior install required)
Repository package_galaxy_sequence_utils_1_0_1 revision c38bd3fe9da6 owned by iuc

Name Version Type
biopython 1.67 package
galaxy_sequence_utils 1.0.1 package

Contents of this repository

Name Description Version Minimum Galaxy Version
Trim off 5' or 3' primers 0.0.16 16.01

Categories
Assembly - Tools for working with assemblies
Fasta Manipulation - Tools for manipulating fasta data
Text Manipulation - Tools for manipulating data