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Registration closed July 15.

BCC2020 is online, global, and affordable. The meeting and training are now done, and the CoFest is under way.

The 2020 Bioinformatics Community Conference brings together the Bioinformatics Open Source Conference (BOSC) and the Galaxy Community Conference into a single event featuring training, a meeting, and a CollaborationFest. Events run from July 17 through July 25, and is held in both the eastern and western hemispheres.

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Sunday, July 19 • 11:55 - 12:00
Please contribute to FASTQE so I don’t have to 🍐

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Abstract


The presenter(s) will be available for live Q&A in this session (BCC East).

Andrew Lonsdale1,2,

1 Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia. Email: andrew.lonsdale@petermac.org
2 Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria 3010, Australia

Project Website: http://fastqe.com
Source Codehttps://github.com/lonsbio/fastqe
License: MIT License

FASTQE is a utility for viewing the quality of biological sequence data as emoji . It
takes the FASTQ format, summarises the average quality score per base-position, and
transcribes each ASCII-encoded Phred summary score into a corresponding emoji to see the
good , the bad ,and the ugly of sequencing data.

Initially just a proof of concept at the end of a 2016 PyConAU talk, it has gradually evolved
into a Python package that is also available as a command line program. It can be
installed both via PyPI and Bioconda. When invoked from the command line it can also
display the minimum and maximum quality scores per position, and bin quality
scores into a reduced set of emoji.

Despite little promotion beyond social media (@fastqe), it has gained some popularity.
FASTQE has been used for an undergraduate command line workshop [1], presentations,
and workshops. Surprisingly , there have even been serious uses of the tool. Using
FASTQE, it was found that artefacts in single-cell RNA-seq data can increase the burden of
error correction in cell barcodes, and revealed at least one case of a software bug that
can lead to incorrect barcode correction .

Despite these compelling use cases, FASTQE has a bus-factor of 1. In order to provide
a more valuable tool for bioinformatics training, education and outreach, contributions are
needed. This presentation will demonstrate the functionality of FASTQE, outline the current
status of the project, a roadmap for enhancements, and a call for more contributions to this
open source project. Everyone knows this is a silly idea . This talk will persuade future
contributors that maybe it isn't a silly as it sounds .

[1] Rachael St. Jacques, Max Maza, Sabrina Robertson, Guoqing Lu, Andrew Lonsdale, Ray A Enke (2019). A Fun
Introductory Command Line Exercise: Next Generation Sequencing Quality Analysis with Emoji!. NIBLSE
Incubator: Intro to Command Line Coding Genomics Analysis, (Version 2.0). QUBES Educational Resources.
doi:10.25334/Q4D172

Speakers
AL

Andrew Lonsdale

Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia



Sunday July 19, 2020 11:55 - 12:00 EDT
BOSC
  Meeting-West