QueroBins

Automated Analysis of Metagenome Assembled Genomes of Bacteria and Archaea

Dependencies

• MetaBat2
• CheckM
• GTDB-tk
• CAT/BAT
• SPAdes

Usage

Assembling with 48 threads and using a maximum of 300 GB of memory

python3 QueroBins.py assemble True --coassembly_table My_Coassembly_Table.tsv --threads 48 --max_memory 300

My_Coassembly_Table.tsv specifies how samples should be coassembled together. It must be a .tsv format file with 4 columns and aheader in the following header: Sample, Group, R1, R2. The contents of the table should specify Sample_ID, Group_ID, path to the R1 file, path to the R2 file. To have a sample be assembled individually (i.e. no coassembly) simply assign it to a group with no other samples.

This command will generate, for each group:

• Assembly_Group_[Group_ID]

Processing pre-assembled scaffold files and filtering scaffolds shorter than 2000 bp

python3 QueroBins.py --assemblies_files Assembly_1.fasta Assembly_2.fasta Assembly_3.fasta... --min_scaffold_length 2000

This command will simply filter out scaffolds shorter than the user defined value and also rename the scaffolds from all assemblies to avoid repeated IDs. Generated files:

• Filtered_Renamed_Assembly_1.fasta, Filtered_Renamed_Assembly_2.fasta, Filtered_Renamed_Assembly_3.fasta...
• Scaffolds_Info.tsv A table with basic infomartion about all the processed scaffolds

Binning scaffolds with MetaBat2

python3 QueroBins.py --assemblies Filtered_Renamed_Assembly_1.fasta Filtered_Renamed_Assembly_2.fasta Filtered_Renamed_Assembly_3.fasta... --make_bins True --binning_method metabat --threads 24

Taxonomy aware binning with CAT and MetaBat2 at the level of phylum

python3 QueroBins.py --assemblies Filtered_Renamed_Assembly_1.fasta Filtered_Renamed_Assembly_2.fasta Filtered_Renamed_Assembly_3.fasta... --make_bins True --tax_aware_binning True --tax_level phylum --binning_method metabat --threads 24

The command above will frist classify contigs taxonomically with CAT, split the assemblies according to contig assigned phylum and perform the binning individiaully on the split files