Workshop on Whole Genome Sequencing and Analysis, 17-19 Sep. 2018

Metagenome Binning

Binning: The process of grouping reads or contigs from metagenomic samples

Binning

Assembly

Declared infectivity against • E. faecalis

• E. faecium

• E. coli

• P. mirabilis

• P. aeruginosa

• S. aureus

What did we do 1. We extracted DNA

2. DNA libraries were sequenced using the Illumina MiSeq platform yielding 250 bp paired-end reads

3. Reads were trimmed and reads mapping to PhiX were removed (using MGMapper)

4. MetaSPAdes were used for assembly

5. Binning were performed with MetaBat

6. Manual checking/correcting of bins based on depth of coverage

# Reads # Reads after trimming

# Reads after PhiX removal

PYO97 5.2 million 2.0 million 1.9 million

PYO2014 18.2 million 6.7 million 6.6 million

Read statistics

Contigs statistics

# Contigs # Longest contig

# Contigs longer than 2000 bp

Percentage of reads that map to the contigs > 2000 bp

PYO97 3005 169,029 bp 179 97,9 %

PYO2014 4165 282,352 bp 270 99,1 %

5.Binning were performed with MetaBat

MetaBat is only available command line

# Bins # Binned bp

PYO97 30 2.7 million (90.2%)

PYO2014 29 2.5 million (90.4%)

Bins statstics

• A total of 30 (PYO97) and 29 (PYO2014) phage draft genomes were discovered in the cocktails

• Of these, 13 (PYO97) and 15 (PYO2014) shared high similarity with known phages

• Eleven draft genomes were common in the two cocktails

• Representatives of phages targeting E. faecalis, E. faecium, E. coli, Proteus, P. auruginosa, and S. aureus were identified

Conclusion

Demonstration: Metagenome binning of bacteria using PATRIC

SRS585831_meta_binning

For a full description of the different analyses that are automatically performed on the bins see: https://docs.patricbrc.org/tutorial/private_genome/private_genome.html

Downloading the bins

https://docs.patricbrc.org/tutorial/index.html