MetaComp --- A flexible pipeline for evaluating metagenome assemblies by integrating different algorithms.

E-mail: heruiliao2-c@my.cityu.edu.hk

Version: V1.0

---

Dependencies

• Python >=2.6
• MaxBin 2.2.4
• BWA 0.7.17
• Quast v5.0.0
• Checkm v1.0.12
• Kraken 0.10.6
• Aragorn v1.2.38
• Barrnap 0.9 Make sure these programs have been added in path

Install(Only for linux)

Install required python libraries: pip install pandas numpy rpy2 matplotlib seaborn pyecharts==0.5.11

git clone https://github.com/liaoherui/MetaComp.git

Usage

python MetaComp.py -l data.list -o out_path

optional arguments:

-l :
We need a list file including five columns with (tab as delimiter).
column 1: Sample id
column 2: Assembly id
column 3: Assembly sequences (.fasta)
column 4: Forward reads (.fastq for short-reads sequencing)/Long reads (.fastq)
column 5 (Option): Reverse reads (.fastq for short-reads sequencing)
This example provides four assemblies for the sample of "hlj"

list/contig_raw_reads.list

-o :
Output path.

Output

MetaComp generates both html report and standalone png figures

• 1.Bin Quality Bar
• 2.Bin Quality Stack Bar
• 3.Bin Completeness/Contamination Scatter
• 4.Taxomony UpSet
• 5.Bin N50 and Coverage Boxplot
• 6.Taxonomy Relative Abundance

References:

how to cite this tool:

Zhang, L., Fang, X., Liao, H. et al. A comprehensive investigation of metagenome assembly by linked-read sequencing. Microbiome 8, 156 (2020). https://doi.org/10.1186/s40168-020-00929-3