Amirhossein Afshinfard

A very minor addition: when users set a maxScaff value, the coverage is variable based on overall length of those `maxScaff` scaffolds. This makes the code to output the resulting...

guppy v6

16

Just wanted to ask if there are any plans on releasing a `guppy >= v6` base calling of the reads? Thanks.

Feature: converting graphs to GFA

1

Thank you for your work on `gfapy`; In the documentation, I could not find a function to convert well-known graph data structures like `igraph` or `networkx` to `gfa`. Assume that...

By default, `seqtk hpc input.fq` will homopolymer compress the input fastq file and also convert it into a fasta file and drop the quality scores. I understand that keeping scores...

Hi Thank you for your work on `gfatools`, I have an assembly graph that I want to process with `gfatools asm` (to simplify the graph, like popping the bubbles, etc)...

AttributeError: module 'scipy.sparse' has no attribute 'coo_array'

6

This is due to `scipy` and `networkx` conflicts. **Solution:** As a workaround, I figured out that we should **either** have `scipy` and `networkx` recent versions, `scipy v1.8` at least **or**...

Indexlr mx filter

2

For filtering some unwanted minimizer kmers, we used to mask them (disqualifying them from generating minimizes by setting their hash value to max) which allowed some other adjacent kmers to...

When I clone the `master` branch, and run `meson build & cd build & ninja test` one test fails with the following information: ``` . . . 9/15 seq_reader_sam_module FAIL...