Brian Bushnell

I still spend all of my time developing BBTools. However, due to internal politics, the JGI website has changed to not feature any JGI-developed bioinformatics software (BBTools, MetaHipmer, etc). Feel free to send an email to JGI's director (nmouncey@lbl.gov) if you think it is helpful for JGI's users to have bioinformatics software such as BBTools on its website, because helping users is supposed to be our goal.

Found the problem in the parser; it will be fixed in 39.20.

OK! I'll look into it and get back to you.

That's odd; looks to me like it should be working. What version are you using?

39.15 is out now.

reformat.sh producing output with 4 reads having the same id

Hmmm... looks like the issue here is that the intermediate fastq file is not really interleaved. Sam/bam files are not interleaved in the first place and should never be treated as such; the order of records is arbitrary and reformatting them as fastq (with samtools) doesn't change that. If you force Reformat to process a noninterleaved file as interleaved, strange things will happen; in this case, the records for that pair are nonadjacent and that causes the header replication, as per the sam specification...

Issues when reading IDs with UMIs