Description

Build a bucketed 3-way Cuckoo hash table index from host and graft reference FASTA files for xenograft read sorting.

Input

name:type
description
pattern

meta

:map

Groovy Map containing host reference information e.g. [ id:'host_ref' ]

host_fasta

:file

Reference FASTA file(s) for the host organism.

*.{fasta,fa,fasta.gz,fa.gz,fasta.bz2,fa.bz2,fasta.xz,fa.xz}

meta2

:map

Groovy Map containing graft reference information e.g. [ id:'graft_ref' ]

graft_fasta

:file

Reference FASTA file(s) for the graft organism.

*.{fasta,fa,fasta.gz,fa.gz,fasta.bz2,fa.bz2,fasta.xz,fa.xz}

nobjects

:integer

Estimated total number of k-mers to be stored in the hash table.

Output

name:type
description
pattern

hash

meta2

:map

Groovy Map containing metadata from the graft or combined reference.

*.hash

:file

Binary Cuckoo hash table file.

*.hash

info

meta2

:map

Groovy Map containing metadata from the graft or combined reference.

*.info

:file

Header and metadata file containing hash table parameters.

*.info

versions_xengsort

${task.process}

:string

The name of the process

xengsort

:string

The name of the tool

xengsort --version

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The name of the process

xengsort

:string

The name of the tool

xengsort --version

:eval

The expression to obtain the version of the tool

Tools

xengsort
MIT

Fast lightweight accurate xenograft sorting using 3-way bucketed Cuckoo hashing

gitlab.com/genomeinformatics/xengsort 10.4230/LIPIcs.WABI.2020.4
maintainer
Github user LeonHornich
get in touch
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