Description

Run the core steps of the sanger-tol/telomere toolkit.

Input

Name
Description
Pattern

meta (map)

Groovy Map containing sample information e.g. [ id:'sample1' ]

reference (file)

Assembly for telomere.

*.{fa,fna,fasta}

telomereseq (string)

DNA sequence of a telomere motif

split_windows (boolean)

Run FindTelomereWindows in split mode

Output

Name
Description
Pattern

telomere

meta (map)

Groovy Map containing sample information

*.telomere (file)

Motif-hit intervals

*.telomere

windows_all

meta (map)

Groovy Map containing sample information

*.all.windows (file)

Telomere density windows

*.all.windows

windows_fwd

meta (map)

Groovy Map containing sample information

*.fwd.windows (file)

Forward windows

*.fwd.windows

windows_rev

meta (map)

Groovy Map containing sample information

*.rev.windows (file)

Reverse windows

*.rev.windows

versions_java

${task.process} (string)

The process the versions were collected from

java (string)

The tool name

java -version 2>&1 | head -n 1 | cut -d '"' -f2 (eval)

The expression to obtain the version of the tool

telomere_bed_fwd

meta (map)

Groovy Map containing sample information

*.fwd.telomere.bed (file)

Forward telomeric intervals

*.fwd.telomere.bed

telomere_bed_rev

meta (map)

Groovy Map containing sample information

*.rev.telomere.bed (file)

Reverse telomeric intervals

*.rev.telomere.bed

versions_find_telomere

${task.process} (string)

The process the versions were collected from

find_telomere (string)

The tool name

0.0.2 (string)

The expression to obtain the version of the tool

Topics

Name
Description
Pattern

versions

${task.process} (string)

The process the versions were collected from

java (string)

The tool name

java -version 2>&1 | head -n 1 | cut -d '"' -f2 (eval)

The expression to obtain the version of the tool

${task.process} (string)

The process the versions were collected from

find_telomere (string)

The tool name

0.0.2 (string)

The expression to obtain the version of the tool

Tools

find_telomere Documentation

Scan the assembly for a telomeric repeat motif (default TTAGGG) on both strands.

License: BSD-3-Clause

FindTelomereWindows Documentation

Slide windows along scaffolds and flag regions where telomeric hits exceed a density threshold.

License: BSD-3-Clause
Authors