Thanks for the great software! We are using metator within our metagenomics pipeline: https://github.com/sanger-tol/metagenomeassembly
Within the pipeline, we use our own Hi-C mapping workflow that maps reads to an assembly with either bwa-mem2 with -5SP or minimap2 and the Arima filter_five_end.pl script (https://github.com/ArimaGenomics/mapping_pipeline/blob/master/filter_five_end.pl), co-ordinate sorts the reads and marks duplicates for removal, before name sorting. The pairs are mapped independently of one another.
Currently, I am processing the BAM file output from this process using bioawk, filtering the BAM to keep either forward or reverse reads and then removing the mate information from the flag (bioawk -c sam '{ \$flag = and(\$flag , 3860 ) ; print \$0 }').
This results in a lot of duplicated space on disk, as we store multiple copies of each file. Would it be possible to enable metator to read all the pairs from a single name-sorted BAM file?
Thanks for the great software! We are using metator within our metagenomics pipeline: https://github.com/sanger-tol/metagenomeassembly
Within the pipeline, we use our own Hi-C mapping workflow that maps reads to an assembly with either bwa-mem2 with
-5SPor minimap2 and the Arima filter_five_end.pl script (https://github.com/ArimaGenomics/mapping_pipeline/blob/master/filter_five_end.pl), co-ordinate sorts the reads and marks duplicates for removal, before name sorting. The pairs are mapped independently of one another.Currently, I am processing the BAM file output from this process using bioawk, filtering the BAM to keep either forward or reverse reads and then removing the mate information from the flag (
bioawk -c sam '{ \$flag = and(\$flag , 3860 ) ; print \$0 }').This results in a lot of duplicated space on disk, as we store multiple copies of each file. Would it be possible to enable metator to read all the pairs from a single name-sorted BAM file?