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katholt / srst2

Short Read Sequence Typing for Bacterial Pathogens
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read input problems #103

Closed JeremyHorst closed 6 years ago

JeremyHorst commented 6 years ago

Hi Mike, holler at the old Samudrala group at UW.

  1. The forward & reverse entry option is not working - just ends without running, says its done.
  2. The requirements for filenames for --input_pe does not actually follow the format you describe, and really really should not be so stringent. Please allow any file name for read1 & read2. There are many things that folks will do to the reads before giving them to this script, which are often tracked in filenames, such as debarcoding, quality filtering, etc.
katholt commented 6 years ago

You can name reads however you like, but as most people are working with batches of paired read files you need to tell the program how to identify/match forward and reverse read files for the same sample.