adoni5/readfishsummarise

About me

Hi! I'm currently (10/11/2022) a post-graduate researcher at the University of Nottingham working on adaptive sampling with nanopore sequencing. I'm interested in all sorts of Bioinformatics, visualisations and fun side projects ( Some of which I even complete ).

Current mood

Current Projects

🐱‍💻 I'm currently working on:

minoTour - real-time monitoring of nanopore sequencers

Swordfish - An inter-communicator for minoTour and readfish

Advent Of Code 🎅🎅 - Just gotta love it

🔭 How to reach me:

Follow me on twitter for utter silence @rorymatics ◦ Follow me on mastadon [email protected] ◦ Open issues! ◦ 📧 [email protected]

readfishsummarise's Issues

Create Python 3.12 wheel

Currently stuck at python<=3.11 in the maturin-action setup in CI.
Check/implement building for a 3.12 interpreter!

Add README.md please

• Installation instructions
• Example usage
• Example output

Summarise enhancements

• Count reads instead of alignments - pay attention to no_map decision
• Add mapped and unmapped read counts
• Add no_map contig to contigs table - pay attention to no_map decision
• Make float of estimated coverage
• Make all the class methods a trait and then hang myself

Estimated coverage is vulnerable to long reads

Long reads will skew the coverage as the yield counts the length of the read over the target region and not the size of the region.

So a 1MB read over a 1kb target will be 100x coverage, not 1x.

We should sum the min of length of the target region or the length of the read.

Switch from flate 2 to gzp

Investigate using gzp multithreaded writer
https://github.com/sstadick/gzp

Per Target coverage

Need to think about this a little more, but I'm sort of envisaging a CSV with each target (contig,start,stop,strand, coverage) as a row. For targets that are on both strands and have the same start stop, we combine them, and list the strand as a .

Problems to solve:

1. When we decide action, we use an any on all targets, so need to know which target we are using.
2. Clip reads if they extend out of the target
3. Would still be an average based on yield and distance.