Running metabat2 on existing JGI assemblies

[Former user]

Hi, I want to update my MAG predictions from 28 metagenomes JGI originally binned using an older version (pre 2) of metabat. I don't really want to download the SAM files (~30-40 GB each). Can I use the contig.cov file provided by JGI and convert it to the appropriate format for the depth.txt file? Thanks, Jeff

*contig.cov #ID Avg_fold Length Ref_GC Covered_percent Covered_bases Plus_reads Minus_reads Read_GC Median_fold Std_Dev scaffold_1_c1 36.4225 721673 0.5845 100.0000 721673 87126 87002 0.5828 36 7.90

depth.txt contigName contigLen totalAvgDepth contigs-1000.fastq.bam contigs-1000.fastq.bam-var NODE_1_length_5374_cov_8.558988 5404 14.2158 14.2158 16.817

[Rob Egan]

You can certainly try that, but running with the BAM files is the preferred and recommended method, as that has a different algorithm for calculating the coverage -- filtering out poorly mapped reads (such as to a different strain), eliminating secondary mappings (such as to repetitive regions) and adjusting for edge effects (where mappers have trouble finding a good seed).