David Eccles (gringer)

Truncated octahedron infill

3

This is the backend code for 3D Honeycomb / Truncated Octahedron infill, as seen in Slic3r (but not [yet] PrusaSlicer). The infill pattern only bridges once per "module", at the...

This is essentially the same as my PrusaSlicer 3D Honeycomb update, with a few little grammar tweaks to fit a little bit nicer into Slic3r. The main visible fix is...

merill-merge: improve building instructions for [Debian] Linux

1

**Describe the bug** Slic3r won't build properly on my Debian system using the recommended instructions for UNIX/Linux. The following errors are seen: ``` $ cmake .. ... CMake Error at...

Basecall models - modbases and research models

1

Question from ONT community by Gabriel Wagner (Med Uni Graz): > I was just wondering, if someone evaluated the new Bonito CRF research models compared to HAC basecalling in case...

Feature request (Alevin): add rhapsody barcode mode

4

There has been a small amount of discussion about the BD Rhapsody barcode / sequence format (e.g. see [here](https://github.com/COMBINE-lab/salmon/issues/445#issuecomment-551083490)), but it would be great if the option could be integrated...

Allow multiple fastq files from the same sample to be used in a single nanopolish run

2

I've got multiple sequencing runs from the same source that I'd like to use with nanopolish (in separate directories). It'd be useful if I could specify these runs separately in...

Add reference-relative variant colouring to the pileup renderer

1

After seeing the neat base colouring for pileups (#2847), I'm wondering if a representation that takes into consideration the type of variant (relative to the reference) would be possible. The...

Canu + minimap for correction on Guppy v3.6 reads: uncorrected has better error profile

6

A pileup of uncorrected Guppy v3.6 reads produces a better guess at the true sequence compared to corrected reads. The errors are in deletion variants and only in specific locations;...

Feature: option to filter dataset based on quality, rather than length

1

My most recent exploration of nanopore data has indicated that the mean base quality reported in the fastq files has a very good correlation with gap-compressed identities when mapping to...

cDNA sequences / genomecov: ignore local deletions, split on large deletions / exon skips

3

[this comment](https://github.com/arq5x/bedtools2/blob/67d5cd8f9ca10556688a8331a73cc8fc604191d1/src/genomeCoverageBed/genomeCoverageBed.cpp#L348) states "we always want to split blocks when a D CIGAR op is found". I have a situation where I *don't* want that to happen. I'm mapping nanopore...