Platanus

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Description

Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from massively parallel shotgun sequencing data.

The pre-processing tools for genome assembling, called Platnaus_trim and Platanus_internal_trim are now available. Platanus_trim is a tool for trimming adaptor sequences and low quality regions. In contrast, Platanus_internal_trim is a tool for trimming internal adaptor sequence, adaptor sequences, and low quality regions. Platanus_trim is designed for paired-end library and Platanus_internal_trim is for mate-pair library.

Platanus-allee (formerly known by Platanus2)

Platanus-allee is an assembler derived from Platanus assembler, however, it was developed with another concept. Platanus-allee tries to construct each haplotype sequence from the beginning and pair them as homologous chromosomes, while Platanus constructs consensus sequence of homologous chromosomes at first and tries to split into each haplotype sequence. Therefore, Platanus-allee marks better performance for highly heterozygous species genome or highly diverged genomic regions. However, for low heterozygous species genome (as a guide < 1.0 %), Platanus assembler would mark better performance than Platanus-allee. This may be caused by the sequence coverage for the target sequence. Platanus-allee targets each haplotype, therefore, simply speaking, it requires a double number of reads.

License

GNU GPL v3

Usage

Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules

to your script before loading a module. Then, you can list all versions of platanus and load default version of platanus as

module avail platanus/ # list available modules
module load platanus   # load (default) module


If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail platanus

and choose explicit version you want to use.

Platanus-allee for some tasks require Minimap and/or LongRanger (see below and help).

module add platanus-1.2.4
platanus # See basic help
# Platanus-allee (Platanus 2)
module add minimap-2.17 # Only required to use PacBio/Oxford-Nanopore long reads
module add longranger-2.2.2 # Only required to prepare 10X linked-reads input (barcoded.fastq)
module add platanus-2.2.2 # Platanus-allee (Platanus 2) itself
platanus_allee # See basic help

Documentation

Homepage