create tiny reference metagenome

[colindaven]

CD TODO
@LisaHollstein FYI

for testing, plots + growth rates require data which isn't sufficient at present

• streptococcus
• rothia
• tiny human chr part of chr22

[colindaven]

done here with mock ref genomes

https://github.com/colindaven/ref_testing

[colindaven]

Let me know @LisaHollstein if you have any problems testing with this reference.

I use part of the public data file
SRR11207337_R1.fastq
for testing against this reference.

More exactly, make a fastq input file from the larger FASTQ using head

wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR112/037/SRR11207337/SRR11207337_1.fastq.gz -o SRR11207337_mock_R1.fastq.gz
gunzip SRR11207337_mock_R1.fastq
head -n 2000000 SRR11207337_mock_R1.fastq > public_mock_sm_R1.fastq

#also a very small version for rapid testing
head -n 90000 SRR11207337_mock_R1.fastq > public_mock_vsm_R1.fastq

This very small vsm dataset gives this sort of number of aligned reads - 4300, 2660. This might be enough for testing. I'll gzip and add it to the repo as well under the test dir.

Pseudomonas_aeruginosa_complete_genome  6792330 4300    0
tig00000001     1480242 25      0
tig00000003     1076883 19      0

Salmonella_enterica_chromosome  4759746 2660    0
Staphylococcus_aureus_chromosome        2718780 2057    0

If you don't want to build/get a new test reference fasta :

You can use the full 2021_12 reference though if you like as well? Will be slower though.

[colindaven]

I added these fastq.gz datasets with
19076bd