Smaps

A pipeline based on unmapped reads, which combines different tools for extends contigs and closing gaps present in the genomes.

Requirements

Linux (64-bit or 32-bit with slightly limited functionality) - The peak RAM usage of this pipeline is about 8GB.
Python3 or higher.
Java version 1.8.0_201 or higher.
Quast in PATH variable.
Perl language installed.
Prokka in PATH variable

Installation

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.