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testing an other reference genome for listeria #3

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huguesrichard opened this issue Sep 23, 2023 · 0 comments

huguesrichard commented Sep 23, 2023

On the visualisation part

2023-GHPP-SGS-Nanopore-Metagenomics/day-metagenomic-classification/hands-on.md

Line 31 in b82c55b

### Visualization of the mapping (IGV)

Possible questions:
Question 1 :

we could add the gene annotation from NCBI: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/196/035/GCF_000196035.1_ASM19603v1/GCF_000196035.1_ASM19603v1_genomic.gff.gz

Question 2:

we could propose to change the ref genome to the one with the best alignment using blast
-https://www.ncbi.nlm.nih.gov/nuccore/CP006596.2?report=fasta

The alignment looks with much less mutations now, and we can see the typical errors from the nanopore reads (indels)

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