(I) Genomes for comparative genomics (fast, only one group)

[mrshu]

• Download genomes of additional Malassezia species (other than malGlo and malSym)
• Use list here [3], download M. pachydermatis, M. nana, M. equina, M. caprae, M. dermatis, M. restricta
  • Download one representative assembly per species (some species have multipe strains /assemblies)
• Rename chromosomes similarly as in A, name fasta files in a systematic way (malPac1.fa etc.)
• Store files in a directory at genomika server
• Do not forget to note down in your documentation the URL of each downloaded fasta file.

[mrshu]

I did download the respective files, here are the endpoints/URLs:

• https://www.ncbi.nlm.nih.gov/genome/39880 ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/278/385/GCF_001278385.1_MalaPachy/GCF_001278385.1_MalaPachy_genomic.fna.gz

• https://www.ncbi.nlm.nih.gov/genome/39879 ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/600/835/GCA_001600835.1_JCM_12085_assembly_v001/GCA_001600835.1_JCM_12085_assembly_v001_genomic.fna.gz

• https://www.ncbi.nlm.nih.gov/genome/39874 ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/264/685/GCA_001264685.1_ASM126468v1/GCA_001264685.1_ASM126468v1_genomic.fna.gz

• https://www.ncbi.nlm.nih.gov/genome/39872 ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/264/625/GCA_001264625.1_ASM126462v1/GCA_001264625.1_ASM126462v1_genomic.fna.gz

• https://www.ncbi.nlm.nih.gov/genome/39873 ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/600/775/GCA_001600775.1_JCM_11348_assembly_v001/GCA_001600775.1_JCM_11348_assembly_v001_genomic.fna.gz

• https://www.ncbi.nlm.nih.gov/genome/702 ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/264/725/GCA_001264725.1_ASM126472v1/GCA_001264725.1_ASM126472v1_genomic.fna.gz

The data is in my home directory on the genomika server.

I am not sure what documentation format would be best suited for this, so I guess we can leave it in this comment for now.

[vidriduch]

@mrshu I believe on last session there was said something about keeping all the data file in specific data folder on genomika server. It is of course open to discusen if we want to follow this convention.

[mrshu]

@vidriduch let's do that. Do you happen to know which folder that would be?

[vidriduch]

@mrshu I believe there should be /data/malGlo folder already created.

[mrshu]

@vidriduch Thanks, I've copied the data there.

I am therefore closing this task as done.

[bbrejova]

I would suggest adding the documentation from this conversation (the list of downloaded files with URLs) to the documentation describing creation of the multiple sequence alignment (task J) so that we have a record from which genomes was the alignment created. Unfortunately this documentation does not exist yet on the wiki.

[mrshu]

@bbrejova thanks for the note, I did add a wiki page to the documentation with the list above.

You can find it here: https://github.com/fmfi-genomika/genomikaMalGlo/wiki/Multiple-whole-genome-alignment

[bbrejova]

Looks good.