README.md

MetaCompass v1.0

Last updated: August 4th, 2018

Publication

Victoria Cepeda, Bo Liu, Mathieu Almeida, Christopher M. Hill, Sergey Koren, Todd J. Treangen, Mihai Pop. bioRxiv 212506; doi: https://doi.org/10.1101/212506

Required software:

• Python3 (>=) 3.1: https://www.python.org/download/releases/3.0/
• snakemake 3.7.1: https://snakemake.readthedocs.io/en/stable/getting_started/installation.html
• BLAST+ (>=) 2.4.0: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST
• bowtie2 (>=) 2.2.9: https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.9
• kmer-mask (May 13th, 2015): https://sourceforge.net/p/kmer/code/HEAD/tree/trunk/
• samtools (>=) 1.x: http://samtools.sourceforge.net/
• MEGAHIT (>=) 1.0.6: https://github.com/voutcn/megahit
• Java runtime (>=) 1.7
• Perl5 (>=) 5.16

Memory and Disk Space Requirements.

You must have at least 13GB of hard disk space to perform a normal installation. You must have 8GB or more memory to allocate to the JVM (used by pilon).

INSTALLATION:

git clone https://github.com/treangen/MetaCompass.git
cd MetaCompass
./install.sh

USAGE

-- I have a set of metagenomic reads, and want to perform reference-guided assembly.

python3 go_metacompass.py -P [read1.fq,read2.fq] -l [max read length]-o [output_folder] -m [min coverage] -t [ncpu]

-- I know the reference genomes, or I want to perform comparative assembly for a particular genome.

python3 go_metacompass.py -r [references.fasta] -P [read1.fq,read2.fq] -o [output_folder] -m [min coverage] -t [ncpu]

OUTPUT

--Output folder contains the following files:

1) metacompass_output folder:
     - Assembled contigs:
            metacompass_output/metacompass.final.ctg.fa
     - Selected Reference genomes sequences:
            metacompass_output/metacompass.recruited.fa  
     - Selected Reference genomes ids and taxonomy ids
            metacompass_output/metacompass.recruited.ids
2) metacompass.tsv file with the following information: 
     - contig ID
     - contig size
     - reference genome used (only reference-guided assembled contigs)
     - name of the genome  

EXAMPLES

Reference-guided assembly with known reference genomes (no reference selection).

-- Input data is available in the tutorial folder:

Reference genome file:  Candidatus_Carsonella_ruddii_HT_Thao2000.fasta
Metagenomic reads:      thao2000.1.fq
                        thao2000.2.fq	

-- Run:

 python3 go_metacompass.py -r tutorial/Candidatus_Carsonella_ruddii_HT_Thao2000.fasta -P tutorial/thao2000.1.fq,tutorial/thao2000.2.fq -o example1_output -m 1 -t 4

Reference-guided assembly with reference selection.

-- Download and extract metagenomic sample:

ftp://public-ftp.hmpdacc.org/Illumina/posterior_fornix/SRS044742.tar.bz2

SRS044742/
    SRS044742.denovo_duplicates_marked.trimmed.1.fastq
    SRS044742.denovo_duplicates_marked.trimmed.2.fastq
    SRS044742.denovo_duplicates_marked.trimmed.singleton.fastq

-- Run:

 python3 go_metacompass.py -P SRS044742/SRS044742.denovo_duplicates_marked.trimmed.1.fastq,SRS044742/SRS044742.denovo_duplicates_marked.trimmed.2.fastq -U SRS044742/SRS044742.denovo_duplicates_marked.trimmed.singleton.fastq -o example2_output

Contact: [email protected]