NAME

       Raptor-upgrade - A fast and space-efficient pre-filter for querying very large collections
       of nucleotide sequences.

SYNOPSIS

       raptor upgrade --input <file> --output <file> [--fpr <number>|--bins <file>]

DESCRIPTION

       Upgrades a Raptor index created with Raptor 2.0 to be compatible with Raptor 3.0.

       The only new parameter need is the false positive rate. The false  positive  rate  affects
       the search results. This can be done in three different ways:

       1) Pass the false positive rate via --fpr.

       2)  The false positive rate can be automatically determined if the paths of the files used
       to build the index are still available.

       3) Pass a file containing the path to the original files, one line  per  file.  The  false
       positive  rate  can  then  be  automatically  determined.  The order of the files does not
       matter. The file with the most k-mers will determine the false positive rate.

OPTIONS

       --fpr (double)
              The false positive rate. Mutually exclusive with --bins. Default: None. Value  must
              be in range [0.000000,1.000000].

       --bins (std::filesystem::path)
              File  containing one file per line per bin. Mutually exclusive with --fpr. Default:
              None. The input file must exist and read permissions must be granted.

       --input (std::filesystem::path)
              The index to upgrade. Parts: Without suffix _0

       --output (std::filesystem::path)
              Path to new index.

   Common options
       -h, --help
              Prints the help page.

       -hh, --advanced-help
              Prints the help page including advanced options.

       --version
              Prints the version information.

       --copyright
              Prints the copyright/license information.

       --export-help (std::string)
              Export the help page information. Value must be one of [html, man, ctd, cwl].

EXAMPLES

       raptor upgrade --input old.index --output new.index

       raptor upgrade --input old.index --output new.index --fpr 0.05

       raptor upgrade --input old.index --output new.index --bins bins.list

VERSION

       Last update: Unavailable
       Raptor-upgrade version: 3.0.1 (commit unavailable)
       Sharg version: 1.1.1
       SeqAn version: 3.3.0-rc.2

URL

       https://github.com/seqan/raptor

LEGAL

       Raptor-upgrade Copyright: BSD 3-Clause License
       Author: Enrico Seiler
       Contact: enrico.seiler@fu-berlin.de
       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.