vSNP Testing Files

This document shows a small dataset that can be downloaded from NCBI SRA. Brief instructions are provided. It includes six Mycobacterium bovis and five Brucella suis biovar 1. Average coverage varies from 60X to 230X. Expect the SRA download to take a couple hours, depending on network speeds. All FASTQ files can be ran together. vSNP will determine the "best reference". VCF output can be compared to the VCF files contained in the zipped files. A successful run will produce VCF files very much if not exactly the same as those provided.

Either the VCF files you create or the files provided in the zipped files can be use to test table generation. Tables output should be very similar if not exactly the same as the tables provided.

Mycobacterium bovis:

00-1MIDNRdeerAlc --> SRR8073662
10-7224_MI_Emm_Beef_48 --> SRR1792265
10-8963_MI_Alco_Beef_47 --> SRR1792271
10-8965_MI_Alco_Beef_47 --> SRR1792272
00-5559_MI_Alco_Beef_9 --> SRR1791698
02-0572_MI_Alco_Beef_18 --> SRR1791772

Brucella suis biovar 1:

B13-0234_zc.vcf --> SRR2058984
B13-0235_zc.vcf --> SRR2058985
B13-0237_zc.vcf --> SRR2058987
B13-0238_zc.vcf --> SRR2058988
B13-0239_zc.vcf --> SRR2058989

Make list...

SRR2058984
SRR2058985
SRR2058987
SRR2058988
SRR2058989
SRR8073662
SRR1792265
SRR1792271
SRR1792272
SRR1791698
SRR1791772

Download FASTQs

for i in `cat list`; do echo $i; fastq-dump --split-files $i; pigz ${i}*.fastq; done

Update names

for i in *_1.fastq.gz; do mv $i ${i%_1.fastq.gz}_R1.fastq.gz; done

for i in *_2.fastq.gz; do mv $i ${i%_2.fastq.gz}_R2.fastq.gz; done

Download Metadata

for i in `cat list`; do wget -O ${i}.csv "http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?save=efetch&db=sra&rettype=runinfo&term= $i"; done

Run vSNP of FASTQ files

Working directory containing downloaded FASTQs

$ vSNP.py

To test reproducibility of step 1 VCF files output can be compared to pre-made VCF files.

Run vSNP on pre-made VCF files

bovis_starting_files.zip
suis1_starting_files.zip

Unzip files, set working directory to contain only VCF files.
Bovis and suis1 VCF files must be ran separately.

Expected table results

Mbovis-01_D20190125_1134-organized-table.xlsx

Bsuis1-09_D20190125_1135-organized-table.xlsx