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katholt / srst2

Short Read Sequence Typing for Bacterial Pathogens
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allow multiple read sets per sample, merged to give single result #16

Closed katholt closed 9 years ago

ppcherng commented 9 years ago

Just wondering, is there any hope of this making it into 0.1.5? My current workaround is to just concatenate all my R1 fastq files together in one file and all my R2 fastq files in another for paired-end samples, but I'd like to avoid this if possible because it takes longer and uses more disk space.

katholt commented 9 years ago

Yes possibly. I'm testing an easy fix now.

katholt commented 9 years ago

Added a simple option (--merge_paired). If this flag is used, SRST2 will assume that all the input reads belong to the same sample. Outputs will be named as [prefix]__combined...

This is currently in master and will be included in 0.1.5.

Note that if you have lots of multi-run read sets, the ease of job submission will depend heavily on how your files are named and you will need to figure out your own approach to manage multiple job submission.

ppcherng commented 9 years ago

I tested this and it seems to work great. However, is there any way to get merging to work with single end samples?