samhunter
commented
11 years ago Setting map_against_reads=True in ARC_config.txt will now map against reads in the first iteration, and not call the assembler. This translates into a process like this:
Iteration 1) Reads are mapped against targets, and extracted to temporary files Temporary files are copied into the targets and renamed Iteration 2) Reads are mapped against the mapped reads from iteration 1 and extracted to temporary files Assemblies are carried out with the reads which map Contigs are copied into the targets and renamed Iteration 3) Reads are mapped against the contigs from iteration 2 and extracted to temporary files Assemblies are carried out with the reads which map If no improvement in number of reads which map is observed, target is removed from further iterations Contigs are copied into targets and renamed Iteration 4) .....etc
Modify map_against_reads behavior so that it includes the contigs AND reads on the 2nd iteration. In other words, it does mapping, attempts to do assemblies, and then includes contigs if any, as well as all reads (assembled or not) as targets for the second round of mapping.