Re: Outreachy project: complete workflows of tools

[Tony Travis <tony.travis@minke-informatics.co.uk>]

On 07/03/2021 23:47, Tassia Camoes Araujo wrote:
> Hi all,
>
> On 2021-03-05 11:09, Tassia Camoes Araujo wrote:
> > [...]
> > Since deadline is approaching quickly, I suggest we move this off-list
> > and start writing in a wiki or pad.
>
> Here is my first draft, pasted below for your reference, but you can
> edit the text directly in this pad:
> https://storm.debian.net/shared/OCYsOOEqJ5-CcfjVxIiye-ex-4LheegyP1pkIFghMKa
>
> Help needed to write the Intern tasks section. Also, please check if you
> have better scientific articles to recommend and list a few tools to be
> used in the starter tasks.
>
> Please help shaping this proposal so it ***really*** makes sense and
> attract interns ;-)

Hi, Tassia.

I recommend using "flexbar", which I use, instead of "Trimmomatic":

> https://github.com/seqan/flexbar

Also, depending on the sequencing technology used, consider assembling 
short-paired-end reads with e.g. Pear:

> https://github.com/tseemann/PEAR

HTH,

  Tony.

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