Nguyen Thanh Nguyen

How does Chromosome scaffolder work?

14

Hi, the script proves to be useful to put the assembled contigs together and reorganize their orientation, but I'm not clear about how it work. I understand the principle that...

Compilation of different preprocessing methods

1

Hi, I've just checked out Shapash. I've seen a lot of this line in the document: `preprocessing=encoder, # Optional: compile step can use inverse_transform method` However, I'm not sure how...

Short Homo Sapien Assembly from Genome in a Bottle Data

10

Hi, I'm trying HASLR using data from GIAB: https://github.com/genome-in-a-bottle/giab_data_indexes/tree/master/NA12878 - All PacBio HIFI reads (~30X), `cat` into a single fastq.gz file. - Subsampled Illumina Short Reads from 300X to 55X,...

[E::bwa_idx_load_from_disk] fail to locate the index files when running

4

Hi, I run the script in https://github.com/humanlongevity/HLA/wiki/BAMs-compatible-with-xHLA to preprocess the file from International Genomes Sample Resource Project, which is mapped to Hg38 with HLA and alternative contigs. However, I got...

HLA Truth set

2

Hi, I want to do some benchmark HLA typing methods, I found out that Illumina Platinum Genomes is a common source of solid validation. However, I haven't found the truth...

Systematically determine `min_dist` and `n_neighbors`

12

I tested multiple combination of `min_dist` and `n_neighbor` on my data, I found that a suitable combination of those hyperparameters can separate the all the cluster(according to labels). I wonder...

Hi, I tried Kourami for HLA typing recently, the tool itself and the preprocessing script run fine on my sample (aligned on Hg38 + decoy + HLA + no ALT)....