Reaper
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Application data |
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| Created by | van Dongen, Stijn |
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| Biological application domain(s) | Next Generation Sequencing |
| Principal bioinformatics method(s) | Sequence contamination filtering, Adapter removal, Sequence trimming, DNA barcoding, Sequencing quality control |
| Technology | Illumina, 454 |
| Created at | EMBL-EBI |
| Maintained? | Yes |
| Input format(s) | (Compressed) FASTA, (Compressed) FASTQ, Tab-delimited, Delimited Text |
| Output format(s) | FASTA, FASTQ, Customizable |
| Software features | Memory efficient and fast. |
| Programming language(s) | C |
| Licence | GPLv3 |
| Operating system(s) | Linux, UNIX, Mac OS X |
Summary: Reaper is a program for demultiplexing, trimming and filtering short read sequencing data.
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Description
Reaper is a fast and highly memory-efficient program written in C, able to process 60-200M reads per hour. It allows tunable identification and stripping of adapter sequences using Smith-Waterman alignments, recognises several types of barcode position and read layout, demultiplexes barcodes, and generates extensive summary statistics including base call quality and tri-nucleotide complexity scores that can be used to perform quality control. Users can specify their own input and output formats in a simple specification language. By default Reaper expects FASTQ input, that may have been compressed. Reaper has been designed to address complex experimental designs and allow filtering based on a range of parameters within a single iteration of the software with minimal impact on speed and memory requirements. Reaper is shipped with tally, a program for uniquifying reads that is optimised to minimise memory usage by compressing sequences in memory.
Links
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