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slamM

A 'step-down' hybrid metagenome assembly pipeline

slamM is no-longer being receiving major updates, though minor updates/bug-fixes may be made. For ACE users, it is recommended you use newer servers.

Requirements

  • snakemake (last tested with ver. 5.32.0)
  • miniconda (last tested with ver. 1.1)

Installation

Install miniconda3 and snakemake (if required)

$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
$ bash Miniconda3-latest-Linux-x86_64.sh
$ conda install -c bioconda -c conda-forge snakemake

Download the repository

$ cd <where_you_want_it_installed>
$ git clone https://github.com/Ecogenomics/slamM.git

Usage

The easiest way to use snakemake is to pass configuration options straight from the shell

$ cd <install_directory>/slamm
$ snakemake create_webpage --cores 24 --use-conda --config long_reads=nanopore_reads.fastq short_reads_1=illumina.1.fastq short_reads_2=illumina.2.fastq workdir=/path/to/output/files/

If only short_reads_1 is given slamM will assume that the fastq is interleaved paired-end reads

Alternatively you can edit config.yaml to point to reads and directory and then run

$ snakemake create_webpage --cores 24 --use-conda