CLUSTpred: Cluster Sequences with VSEARCH

In HajkD/LTRpred: De novo functional annotation of retrotransposons

Cluster Sequences with VSEARCH

Description

Cluster putative LTR transposons predicted by LTRpred using VSEARCH.

Usage

CLUSTpred(
  file,
  similarity = 0.9,
  strand = "both",
  cores = 1,
  out.name = paste0(basename(file), "_CLUSTpred"),
  output = NULL
)

Arguments

file	path to predicted LTR transposons generated by LTRpred (in fasta format).
similarity	reject if sequence similarity is lower than this threshold.
strand	cluster using plus or both strands.
cores	number of cores that shall be used for parallel computations.
out.name	name of the output files (*.uc, *.log, *.blast6out).
output	path to a folder in which output shall be stored.

Details

To be able to use this function the VSEARCH command line tool needs to be installed.

Value

First the following files generated by VSEARCH are stored in the output folder (default: getwd):

• *.uc USEARCH cluster format generated by VSEARCH storing the sequence cluster information of the input LTR transposons.

• *.log a log file of the VSEARCH run.

• *.blast6out BLAST output generated by VSEARCH storing the BLAST hit information of the input LTR transposons.

A USEARCH cluster format (*.uc file extension) table (see read.uc for specifications).

Author(s)

Hajk-Georg Drost

References

https://github.com/torognes/vsearch

HajkD/LTRpred documentation built on April 22, 2022, 4:35 p.m.