We need some good graphics for the main sampler screen. This is where you can do rudimentary editing of the samples that are played in the sequencer.
There are two screens. The main screen with the controls:

• Volume (this one may be changed later)
• Speed (Playspeed. The sample also pitches up or down)
• Filter (in the middle the sound is unchanged, away from center it engages either hi-pass

Three very minor typos are present in these documents that break the code when copied-and-pasted as they are.

Link: https://gatk.broadinstitute.org/hc/en-us/community/posts/360056484652-Typos-in-docs

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1.  https://gatk.broadinstitute.org/hc/en-us/articles/360036726571-LeftAlignAndTrimVariants

the fifth code block on this page

fastp will overwrite -o without checking if it is the same as -i. Worth adding a check for this scenario.

This would make the process for making small corrections easier for non-developers. From a comment on #8349.

This should be pretty easy to do and a good task for a new developer or community member looking to make a small contribution.

Spotted in the gitter channel

The big thing for me was that it wasn't clear that the cache could be reused. It talks about the state monad and the cache being immutable which caused me to make some bad assumptions, even after diving into the code.

This should be more explicit and clear to not confuse people.

The current implementation of slice md5 validation proceeds in two steps; it first tries to validate the md5 for the entire slice span. If that fails, it falls back to checking the md5 for a smaller span ([terminating one base earlier](https://github.com/

Currently it dies - it should just ask again

[2020-03-14 11:11:41] INFO  Configuration file not found: /Users/Yannick/.sequenceserver.conf

Database dir not set.

SequenceServer needs to know where your FASTA files or BLAST+ databases are.
Please enter the path to the relevant directory (default: current directory).

Press Ctrl+C to quit.

>> ~/db
[2020-03-14 11:21:27] INFO  Conf

Hello!
I ran Prokka and Roary with a set of genomes where some input fasta files had names like Listeria-<sample ID>.fasta and some files had names like Listeria_<sample ID>.fasta (note the difference - - vs _). Sample identifiers were preserved in Prokka output (and hence Roary input) but I noticed that Roary produced output only for the last sample of those whose filenames contained the

I couldn't find a manual page of some sort that explains every parameter being used in snaptools. Some of them are explained in: https://github.com/r3fang/SnapATAC/wiki/FAQs
But some are not clearly written.

For example, in snaptools snap-pre what does --max-num=20000 exactly do? Does it take the top 20k cells with the most cell barcodes?

It would be great if we could set up tests to run through all the jupyter notebooks :)

There are probably some instructions on how to do it here:
https://docs.fast.ai/dev/develop.html

Thanks for the new -C function for counting constant sites...super useful! Can I recommend explicitly stating that the output of -C is in A,C,G,T order in the help message? Some users might not know that alphabetical order is convention.

Your documentation says to use "hg38 reference without alt contigs". Could you provide a link to which reference genome file you used ? I would like to try the same reference genome file. Thanks.