raptor1

Overview

Raptor is a system for approximately searching many queries such as next-generation sequencing reads or transcripts in large collections of nucleotide sequences. Raptor uses winnowing minimizers to define a set of representative k-mers, an extension of the interleaved Bloom filters (IBFs) as a set membership data structure and probabilistic thresholding for minimizers. Our approach allows compression and partitioning of the IBF to enable the effective use of secondary memory.

Subcommands

This program must be invoked with one of the following subcommands:
- build
- layout
- prepare
- search
- upgrade

See the respective help page for further details (e.g. by calling Raptor build -h).

The following options below belong to the top-level parser and need to be specified before the subcommand key word. Every argument after the subcommand key word is passed on to the corresponding sub-parser.

Options

Version

Last update: Unavailable
Raptor version: 3.0.1 (commit unavailable)
Sharg version: 1.1.1
SeqAn version: 3.4.0-rc.3

URL

https://github.com/seqan/raptor

Legal

Raptor Copyright: BSD 3-Clause License
Author: Enrico Seiler
Contact: [email protected]
SeqAn Copyright: 2006-2023 Knut Reinert, FU-Berlin; released under the 3-clause BSDL.
In your academic works please cite: Raptor: A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences; Enrico Seiler, Svenja Mehringer, Mitra Darvish, Etienne Turc, and Knut Reinert; iScience 2021 24 (7): 102782. doi: https://doi.org/10.1016/j.isci.2021.102782
For full copyright and/or warranty information see --copyright.