A pipeline based on unmapped reads, which combines different tools for extends contigs and closing gaps present in the genomes.
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Linux (64-bit or 32-bit with slightly limited functionality) - The peak RAM usage of this pipeline is about 8GB.
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Python3 or higher.
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Java version 1.8.0_201 or higher.
-
Quast in
PATH
variable. -
Perl language installed.
-
Prokka in
PATH
variable
You need to install git
$ sudo apt install git
Clone smaps repository to your machine
$ cd && git clone https://github.com/lucaspompeun/smaps.git
Creat a symbolic link to Smaps
$ sudo chmod 777 smaps/* && ln -s ~/smaps/smaps.py /usr/local/bin/smaps
With all dependecies satisfied you can simple run on terminal
$ smaps -h
usage: smaps.py [-h] -read1 READ1 [-read2 READ2] -output OUTPUT [-gff GFF] [-reference REFERENCE] [-sspace SSPACE] [-minreads MINREADS] [--version]
Smaps A tool to extends contigs to reduce gaps with unmapped reads
optional arguments:
-h, --help show this help message and exit
-read1 READ1 first fastq file (required)
-read2 READ2 second fastq file (optional)
-output OUTPUT output for results files (please, give the full path for the output)
-gff GFF gff file (optional)
-reference REFERENCE reference file (optional)
-sspace SSPACE number of runs of sspace software (optional, default=5)
-minreads MINREADS minimum number of unmapped reads to extend a base (optional, default=5)
--version show program's version number and exit
Please, always submit the input files with pathway to the file.