Sample scripts

The latest version with a seedfile as the input

aws batch submit-job \
  --job-name nf-hybridassembly \
  --job-queue priority-maf-pipelines \
  --job-definition nextflow-production \
  --container-overrides command="FischbachLab/nf-hybridassembly, \
"--seedfile", "s3://genomics-workflow-core/Results/HybridAssembly/BrianYu_20220311/HotspringMatIsolate_Chloroflexus-Stock92-20220203.tsv", \
"--coverage", "100", \
"--output_path", "s3://genomics-workflow-core/Results/HybridAssembly/BrianYu_20220311" "

long reads only assembly *** NOT WORKING using long.nf rather than default name main.nf ***

sampleRate must be greater than 0 and less than 100

aws batch submit-job \
  --job-name nf-hybridassembly \
  --job-queue priority-maf-pipelines \
  --job-definition nextflow-production \
  --container-overrides command="FischbachLab/nf-hybridassembly, \
"--sampleRate", "50", \
"--seedfile", "s3://genomics-workflow-core/Results/HybridAssembly/Nathan_20220301/1.seedfile.tsv", \
"--output_path", "s3://genomics-workflow-core/Results/HybridAssembly/Nathan_20220301/tmp" "

Seedfile example

Note that the seedfile is a tab-separated values file without header

The format is sample_name, prefix(date), short_R1, short_R2 and long_reads

SH0001651-00109 20221021 s3://maf-sequencing/Illumina/MITI-MCB/G04_MITI001_SH0001651_R1.fastq.gz s3://maf-sequencing/Illumina/MITI-MCB/G04_MITI001_SH0001651_R2.fastq.gz s3://maf-sequencing/nanopore/MITI/Combined/SH0001651-00109.combined.fastq.gz

MITI MCB Hybrid assembly example

Final output path: s3://genomics-workflow-core/Results/HybridAssembly/MITI-MCB/sample_name/prefix/

aws batch submit-job \
  --job-name nf-hybridassembly \
  --job-queue priority-maf-pipelines \
  --job-definition nextflow-production \
  --container-overrides command="FischbachLab/nf-hybridassembly, \
"--seedfile", "s3://genomics-workflow-core/Results/HybridAssembly/20221018.11.seedfile.tsv", \
"--output_path", "s3://genomics-workflow-core/Results/HybridAssembly/MITI-MCB" "

The draft assembly is further polished by

[Polypolish] (https://github.com/rrwick/Polypolish): short-read polisher for long reads. The polished assembly can be found in the folder UNICYCLER_POLISHED