Hadrien Gourlé

presets

1

In light of reviewer 3's comments but only vaguely related, it would be a great addition to allow presets of "known" microbiomes to be simulated, i.e. `iss generate --model miseq...

# Overview the goal of the project is to create a (meta)genomics reads simulator, i.e. a program capable of simulating realistic high-throughput sequencing data This issue is aimed at being...

This issue summarises the discussion that emerged at the London hackathon concerning a possible merge with [YAMP](https://github.com/alesssia/YAMP) While MAG focuses heavily on assembly, YAMP is assembly-free and focuses on taxonomy...

Hi, I'm using `bionode-ncbi` to download a large number of files from the SRA. It has been working very well so far except for 54 samples, all belonging to the...

Hi, I know I'm doing unspeakable things with terrible input data but hear me out. We've had an issue in a production pipeline where some runs would stall and never...

temporary vcfs are not cleaned up

1

if `-M` is not provided, `*.iss.tmp.{N}.vcf` files should be removed

Ubiome R notebook

6

*Ready for testing* - [x] install and load necessary packages - [x] build data frame containing info about public data - [x] load public data files - [x] exploratory analysis...

I'm planning to add hyrbid assembly capabilities to nanoflow. This issue will serve as to-do list - [ ] illumina read trimming - [ ] hybrid assembly with unicycler -...

assign Ensemble gene ids to transcripts

3

in the RNA seq tutorial in this code block ```R txdb