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SeqPrep (version 0.1)

Forward reads:

Reverse reads:

Save discarded reads?:

Forward read primer/adapter sequence to trim as it would appear at the end of a read:

default (genomic non-multiplexed adapter1) = AGATCGGAAGAGCGGTTCAG. See help for more details

Reverse read primer/adapter sequence to trim as it would appear at the end of a read:

default (genomic non-multiplexed adapter2) = AGATCGGAAGAGCGTCGTGT. See help for more details

Quality score cutoff for mismatches to be counted in overlap:

Default = 13

Minimum length of a trimmed or merged read to print it:

Default = 30

Show extended options?:

Merge overlapping reads and output merged reads?:

Maximum quality score in merged output:

In phred 33. Default (']') is 60

Minimum overall base pair overlap to merge two reads:

Default = 15

Maximum fraction of good quality mismatching bases to overlap reads:

Default = 0.02

Minimum fraction of matching bases to overlap reads:

Default = 0.9

Output stats of sequence lengths?:

What it does

SeqPrep is a program to merge paired end Illumina reads that are overlapping into a single longer read. It may also just be used for its adapter trimming feature without doing any paired end overlap. When an adapter sequence is present, that means that the two reads must overlap (in most cases) so they are forcefully merged. When reads do not have adapter sequence they must be treated with care when doing the merging, so a much more specific approach is taken. The default parameters were chosen with specificity in mind, so that they could be ran on libraries where very few reads are expected to overlap. It is always safest though to save the overlapping procedure for libraries where you have some prior knowledge that a significant portion of the reads will have some overlap.

Before running SeqPrep make sure to check that the program's defaults are indeed the adapters you are looking for. Try copying the default forward adapter from this file and grep it against your reads doing a word count, also try the same with the reverse adapter with grep. You should see some hits. You can also try using (and validating with grep) -A GATCGGAAGAGCACACG -B AGATCGGAAGAGCGTCGT as parameters. To find a list of Illumina adapter sequences you should write to Illumina tech support TechSupport@illumina.com (they do not like people to share the list of sequences outside of their institution).

You can also try to search online for Illumina read primers, of course.

See more details on SeqPrep github repository: https://github.com/jstjohn/SeqPrep

License

SeqPrep is copyrighted to John St. John.

This wrapper is copyrighted by Lionel Guy, and is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.