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kraken-build - Online in the Cloud

Run kraken-build in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command kraken-build that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


kraken-build - assigning taxonomic labels to short DNA sequences

SYNOPSIS


kraken-build [task option] [options]

DESCRIPTION


Task options (exactly one must be selected):
--download-taxonomy
Download NCBI taxonomic information

--download-library TYPE
Download partial library (TYPE = one of "bacteria", "plasmids", "viruses", "human")

--add-to-library FILE
Add FILE to library

--build
Create DB from library (requires taxonomy d/l'ed and at least one file in library)

--rebuild
Create DB from library like --build, but remove existing non-library/taxonomy files
before build

--clean
Remove unneeded files from a built database

--shrink NEW_CT
Shrink an existing DB to have only NEW_CT k-mers

--standard
Download and create default database

--upgrade
Upgrade an existing older database to use scrambled minimizer ordering (see README
for details)

--help Print this message

--version
Print version information

OPTIONS


--db NAME
Kraken DB/library name (mandatory except for --help/--version)

--threads #
Number of threads (def: 1)

--new-db NAME
New Kraken DB name (shrink task only; mandatory for shrink task)

--kmer-len NUM
K-mer length in bp (build/shrink tasks only; def: 31)

--minimizer-len NUM
Minimizer length in bp (build/shrink tasks only; def: 15)

--jellyfish-hash-size STR
Pass a specific hash size argument to jellyfish when building database (build task
only)

--max-db-size SIZE
Shrink the DB before full build, making sure database and index together use <=
SIZE gigabytes (build task only)

--shrink-block-offset NUM
When shrinking, select the k-mer that is NUM positions from the end of a block of
k-mers (default: 1)

--work-on-disk
Perform most operations on disk rather than in RAM (will slow down build in most
cases)

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