John Didion

Also - make this automatic.

Thanks for this report. On first glance, I like option 1 but I'll need to consider it a bit. In the meantime, a workaround is to write the orphaned reads...

Great! Note that it’s only sampling 10k reads. If adapters contamination is rare, you may need to increase the sample size (using the —maxreads option). > On May 12, 2017,...

@jfear the 'sra' branch of Atropos now includes direct streaming from an SRA accession using the '-sra' option. You need to have [ngs-python](https://github.com/ncbi/ngs/tree/master/ngs-python) installed.

Nope, no estimate. I've started a new job recently and the amount of free time I have for this and other projects is highly variable. Contributions are always welcome.

This issue is partially duplicated by #60 and #65. @jfear @antonkulaga, do you think if those two issues are implemented, that will solve the use case for this issue?

Yes that’s right. > On Mar 16, 2018, at 7:09 PM, Justin Fear wrote: > > Sounds interesting, I think it would address the use case. This will only work...

Thanks for reporting this. As you've probably figured out, Atropos tries to use system gzip for compression when available, because it's much faster than using the python gzip module. However,...

Thanks! Atropos actually does take a config file right now, it's just not documented yet. The format is pretty simple right now - just put one argument per line. The...

I like this idea. Rather than copy over the -l option from cutadapt, I think I can repurpose -u/-U in such a way as to support the current usage while...