Assemble a genome and evaluate the result [Link]

There is a new page on the bioboxes site (such a great name!) which details how bioboxes can be used to assemble a genome and then evaluate the results:

A common task in genomics is to assemble a FASTQ file of reads into a genome assembly and followed by evaluating the quality of this assembly. This recipe will explore using bioboxes to do this task.

A third Assemblathon contest came very close to launching earlier this year…except that it didn't — maybe this will be the subject of a future blog post! — and we planned to make biobox containers a requisite part of submitting assemblies. If Assemblathon 3 ever gets off the ground I feel happier knowing that the bioboxes team is doing so much great work that will make running such a contest easier to manage.

Time to toggle the JABBA-award status of this bioinformatics software name

Give me a B.
Give me a O.
Give me a G.
Give me a U.
Give me a S.

What have you got?

Another BOGUS bioinformatics acronym! This time it is courtesy of the journal BMC Bioinformatics:

I think you can already see why this one is going to win a JABBA award. The name 'TOGGLE' derives from TOolbox for Generic nGs anaLysEs. Using their same strategy, they could have also gone for BOGGLE, BONNY, or even BORINGLY.

How to ask for bioinformatics help online

Part two of a two-part series.

In part one I covered where to ask for bioinformatics help. Now it is time to turn to the issue of how you should go about asking for help. Hat tip to reader Venu Thatikonda (@nerd_yie) for pointing me out to this 2011 PLOS Computational Biology article that tackles similar ground to this blog post. Here are my five main suggestions, with the last one being further broken down into 9 different tips:

  1. Be polite. Posting a question to an online forum does not mean that you deserve to be answered. If people do answer, they are usually doing so by giving up their own free time to try to help you. Don't berate people for their answers, or insult them in any way.
  2. Be relevant. Choose the right forum in which to ask your question. Sites like SEQanswers have different forums that discuss particular topics, so don't post your PacBio question in the Ion Torrent forum.
  3. Be aware of the rules. Most online forums will have some rules, guidelines, and/or an FAQ which covers general posting etiquette and other things that you should know. It is a good idea to check this before posting on a site for the first time.
  4. Be clever. Search the forum before asking your question, there is often a good chance that your question has already been asked (and answered) by others.
  5. Be helpful. The biggest thing you can probably do in order to get a useful answer to a question is to provide as many useful details as possible, these include:
    1. Type of operating system and version number, e.g. Mac OS X 10.10.5.
    2. Version number/name of software tool(s) you are using, e.g. NCBI BLAST+ v2.2.26, Perl v5.18.2 etc. A good bioinformatics or Unix tool will have a -v, -V, or --version command-line option that will give you this information.
    3. Any error message that you saw. Report the full error message exactly as it appeared.
    4. Where possible, provide steps that would let someone else reproduce the problem (assuming it is reproducible).
    5. Outline the steps that you have tried, if any, to fix the problem. Don't wait for someone to suggest 'quit and restart your terminal' before you reply 'Already tried that'.
    6. A description of what you were expecting to happen. Some perceived errors are not actually errors at all (the software was doing exactly what was asked of it, though this may not be what the user was expecting).
    7. Any other information that could help someone troubleshoot your problem, e.g. a listing of your Unix terminal before and/or after you ran a command which caused a problem.
    8. A snippet of your data that would allow others to reproduce the problem. You may not be able to upload data to the website in question, but small data snippets could be shared via a Dropbox or Google Drive link, or on sites like Github gist.
    9. Attach a screenshot that illustrates the problem. Many forum sites allow you to add image files to a post.

Any other suggestions?

 

Updates

2015-11-08 09.44: Added link to PLOS Computational Biology article

Gender ratio of speakers at today's Festival of Genomics California conference

The Festival of Genomics Conference California conference starts today. From the speaker lineup I count 132 speakers with a gender ratio of 72.7% men and 27.3% women. This is a good ratio compared to many (most?) genomics conferences — see Jonathan Eisen's many excellent posts on this subject — and it exceeds the background level of women in senior roles in genome institutes around the world (a figure I previously calculated as 23.6%).

However, it was because the ratio of women speakers was below my self-imposed target of 33.3% that I withdrew Front Line Genomic's kind offer of a speaking position and requested that they instead offer my slot to a woman.

I think Front Line Genomics are ahead of many conference organizers in addressing gender bias, and I look forward to seeing the final lineup at their upcoming Festival of Genomics London conference.

This post is to serve as a reminder that we, as a community, still need to do much better at addressing gender bias in our field, and that men can actively help this process by refusing to speak or present at conferences which show extreme bias. Preferably, I would like others to adopt my 33.3% target as a minimum ratio that we should be aiming for (this applies both ways, though there doesn't seem to be much likelihood of men feeling underepresented any time soon).