README

CoPTR is a tool for estimating peak-to-trough ratios from metagenomic sequencing.

References:

https://github.com/tyjo/coptr/

https://coptr.readthedocs.io/en/latest/tutorial.html

Note that only hCom2 database is built for CoPTR. For paired end sequencing, it is recommend to only map reads from a single mate-pair.

Seedfile example

Note that the seedfile is a CSV (comma-separated values) file with header

The format of the seedfile is sample_name,short_R1,short_R2

sampleName,R1,R2
Plate1_MITI-001-Mouse_A10_W8_6-1_S394,s3://maf-sequencing/Illumina/221213_A01679_0069_BHLLVHDSX5/Allison_Weakley/MITI-001-BackfillAnalysis/Plate1_MITI-001-Mouse_A10_W8_6-1_S394_R1.fastq.gz,s3://maf-sequencing/Illumina/221213_A01679_0069_BHLLVHDSX5/Allison_Weakley/MITI-001-BackfillAnalysis/Plate1_MITI-001-Mouse_A10_W8_6-1_S394_R2.fastq.gz

A sample batch submission script

aws batch submit-job \
  --job-name nf-coptr \
  --job-queue priority-maf-pipelines \
  --job-definition nextflow-production \
  --container-overrides command="FischbachLab/nf-coptr, \
"--project", "TEST", \
"--seedfile", "s3://genomics-workflow-core/Results/coptr/230523.seedfile.csv", \
"--outdir", "s3://genomics-workflow-core/Results/coptr" "

The output is a CSV file where, the rows are reference genomes, and the columns are samples. Each entry is the estimated log2 PTR.

The final output file path:

s3://genomics-workflow-core/Results/coptr/TEST/TEST_hcom2_coptr.csv

The plots are available at

s3://genomics-workflow-core/Results/coptr/TEST/plots-dir/