PanTools version 1.3-alpha,
is a java application based on Neo4j graph database community
edition 3.3.1 for computational pan-genomics, developed by
Siavash Sheikhizadeh in Wageningen university, the Netherlands.
If you use PanTools please do not forget to cite it :
https://doi.org/10.1186/s12859-018-2362-4
https://github.com/Sheikhizadeh/pantools
Requirements
-
KMC: is a disk-based programm for counting k-mers from
(possibly gzipped) FASTQ/FASTA files
(http://sun.aei.polsl.pl/kmc).
You need to download it and add the path to the
appropriate version (linux, macos or windows) of kmc
and kmc_tools executables to your OS path environment
variable.
-
Java Virtual Machine version 1.8 or higher: Add the path to
the java executable to your OS path environment variable.
-
MCL: The Markov Cluster Algorithm, is a fast and scalable
unsupervised cluster algorithm for graphs
(http://micans.org/mcl ) which is needed for group
functionality of PanTools.
You need to download, unzip and compile it (see README),
and add the path to the mcl executable to your path
environment variable.
Running the program
java -jar pantools.jar
pantools.jar is available in folder pantools/dist/
arguments is a list of key value pairs separated by whitespace.
JVM options
[-server]
[-XX:+UseConcMarkSweepGC]
[-Xmx(a number followed by g or m)]
PanTools commands
To build a pan-genome out of a set of genomes.
--database_path or -dp
path to the pangenome database.
--genomes-file or -gf
a text file containing paths to FASTA files of genomes;
each in a seperated line.
--kmer-size or -ks
the size of k-mers, if not given or is out of range
(6 <= K_SIZE <= 255),an optimal value would be calculated automatically.
To build a pan-proteome out of a set of proteins.
--database_path or -dp
path to the pangenome database.
--proteomes_file or -pf
a text file containing paths to FASTA files of proteomes;
each in a seperated line.
To add new genomes to an available pan-genome.
--database_path or -dp
path to the pangenome database.
--genomes-file or -gf
a text file containing paths to FASTA files of the new
genomes to be added to the pangeome;
each in a seperated line.
To add new annotations to an available pan-genome.
--database_path or -dp
path to the pangenome database.
--annotations-file or -af
a text file each line of which contains genome number and
path to the corresponding GFF file seperated by one space.
Genomes are numbered in the same order they have been added
to the pangenome. The protein sequence of the annotated genes
will be also stored in the folder "proteins" in the same path
as the pangenome.
--connect_annotations or -ca
connect the annotated genomic features to the nodes of gDBG.
To retrieve the sequence of annotated features from the pangenome.
For each genome the resulting FASTA file will be stored in the current
directory.
--database_path or -dp
path to the pangenome database.
--genome-numbers or -gn
a text file containing genome_numbers for which the features will
be retrieved. The resulting FASTA files have two parts separated by a dot.
The first part determines the feature and the second determines the
genome number; for example, genes.1.fasta.
--feature-type or -ft (default = gene)
the feature name; for example gene, mRNA, exon, tRNA, ...
To retrieve the sequence of some genomic regios from the pangenome.
The results will be stored in the same folder as the pangenome.
--database_path or -dp
path to the pangenome database.
--regions-file or -rf
a text file containing records with genome_number,
sequence_number, begin and end positions seperated by one
space for each region. The resulting FASTA file would have
the same name with an additional .fasta extention.
To retrieve the full sequence of some genomes. The results will be
stored in the same folder as the pangenome itself.
--database_path or -dp
path to the pangenome database.
--genome-numbers or -gn
a text file containing genome_numbers to be retrieved in each line.
The resulting FASTA files are named like Genome_x.fasta.
To add homology nodes which point to a groups of homologous proteins.
--database_path or -dp
path to the pangenome database.
--intersection-rate or -ir (default = 0.09)
the fraction of kmers needs to be shared by two
intersecting proteins. Should be in range [0.001, 0.1].
--min-protein-identity or -mpi (default = 95)
the minimum similarity score. Should be in range [1-99].
--mcl-inflation or -mi (default = 9.6)
the MCL inflation. Should be in range ]1-19[.
--contrast or -ct (default = 8)
the contrast factor. Should be in range ]0-10[.
--relaxation or rn (default 1)
the relaxation in homology calls. Should be in range [1, 8],
from strict to relaxed.
--threads-number or -tn (default = 1)
the number of parallel working threads