Selected scripts and codes used for determining the detection limit and sensitivity of Salmonella .spp in mixed microbially communities using whole meta-/genome amplification (WMA/WGA).
Test data sets included in this repository are from a subset of samples pulled from the ATCC Environmental mock community dataset. Test depth and fastq files are subsampled at depth of 250,000 reads each (merged paired-end).
Align-and-stats.sh map fastq reads to reference using strict mapping threshold and calls bam-statistics.sh to return depth, coverage, and mapping statistics. Set to run in Test_dataset_fastq directory.
Example Usage:
sh Align-and-stats.sh ../Salmonella_REF/Salmonella
Parse_Blast_custom_WGA.py parse BLAST output from FastQ-screen multihit reads using customized ATCC Environmental database and ncbi-blast+. The following format and delimiters are required in the outputs to be parsed:
-outfmt “6 qseqid sacc staxid stitle length pident qcovs mismatch gapopen qstart qend sstart send evalue bitscore” \
Parameters:
-d directory
-s file suffix for blast output results
-mock mock community (Environmental, Zymo, Isolate)
Use with Test_dataset_multihit.
Example Usage:
python Parse_Blast_custom_WGA.py -d Test_dataset_multihit -s _blast-hits.txt -mock Environmental
CV.py return table of calculated coefficient of variation in genome depths based on samtools depth profile outputs. Use with Test_dataset_depth.
Parameters:
-d directory
-s file suffix for depth files
-r gene/contig/plasmid/region on genome
Eample Usage:
python CV.py -d Test_dataset_depth -s _depth.txt -r NC_003197.2
Depth_plots.ipynb create visual depth plots from samtools depth profile outputs. Use with Test_dataset_depth.
In submission
Org: Division of Foodborne Waterborne and Environmental Diseases, WDPB
Version: 1.0.0
Status: Maintained
Keywords: pathogen detection, next generation sequencing analysis, bioinformatics, genomics, whole genome amplification, multiple displacement amplification, metagenomics, Salmonella enterica
Contact Email: ncezid_shareit@cdc.gov