Difference between revisions of "Adapter Removal (software)"
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{{Bioinformatics application | {{Bioinformatics application | ||
|sw summary=Removes adaptor fragments from raw short read sequence data and outputs data to FASTA format. | |sw summary=Removes adaptor fragments from raw short read sequence data and outputs data to FASTA format. | ||
| − | |bio domain= | + | |bio domain=Workflows, |
| − | |bio method=Adapter | + | |bio method=Adapter removal |
| − | |bio tech=Illumina, 454, | + | |bio tech=Illumina, 454, |
|created by=Stocks MB, Mapleson D, Moxon S | |created by=Stocks MB, Mapleson D, Moxon S | ||
|created at=University of East Anglia | |created at=University of East Anglia | ||
|maintained=Yes | |maintained=Yes | ||
| − | |input format=FASTA, FASTQ, | + | |input format=FASTA, FASTQ, |
|output format=FASTA | |output format=FASTA | ||
| − | |sw feature= | + | |sw feature=Sequence trimming, |
| − | |language=Java, | + | |language=Java, |
|licence=Custom Licence | |licence=Custom Licence | ||
| − | |os=Linux 64, Windows, Mac OS X, | + | |os=Linux 64, Windows, Mac OS X, |
}} | }} | ||
== Description == | == Description == | ||
<!-- Describe the application in the space below --> | <!-- Describe the application in the space below --> | ||
| + | Part of the UEA sRNA Workbench freely available at: | ||
| + | |||
| + | http://srna-workbench.cmp.uea.ac.uk | ||
Removes adaptor fragments from raw short read sequence data and outputs data to FASTA format. Output comes in a "non redundant" format compressing all repeated reads into a single read with an abundance count in brackets. | Removes adaptor fragments from raw short read sequence data and outputs data to FASTA format. Output comes in a "non redundant" format compressing all repeated reads into a single read with an abundance count in brackets. | ||
For example: | For example: | ||
| − | > | + | > <br/> |
| − | ACTG | + | ACTG <br/> |
| − | > | + | > <br/> |
| − | ACTG | + | ACTG <br/> |
| − | Becomes: | + | Becomes: <br/> |
| − | >ACTG(2) | + | >ACTG(2)<br/> |
| − | ACTG | + | ACTG |
Latest revision as of 10:40, 11 January 2016
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Application data |
|
| Created by | Stocks MB, Mapleson D, Moxon S |
|---|---|
| Biological application domain(s) | Workflows |
| Principal bioinformatics method(s) | Adapter removal |
| Technology | Illumina, 454 |
| Created at | University of East Anglia |
| Maintained? | Yes |
| Input format(s) | FASTA, FASTQ |
| Output format(s) | FASTA |
| Software features | Sequence trimming |
| Programming language(s) | Java |
| Licence | Custom Licence |
| Operating system(s) | Linux 64, Windows, Mac OS X |
Summary: Removes adaptor fragments from raw short read sequence data and outputs data to FASTA format.
"Error: no local variable "counter" was set." is not a number.
Description
Part of the UEA sRNA Workbench freely available at:
http://srna-workbench.cmp.uea.ac.uk
Removes adaptor fragments from raw short read sequence data and outputs data to FASTA format. Output comes in a "non redundant" format compressing all repeated reads into a single read with an abundance count in brackets. For example:
>
ACTG
>
ACTG
Becomes:
>ACTG(2)
ACTG
Links
References
none specified
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