NCI-CGR / CGR_pacbio_hpylori_analysis_pipeline

Hpylori Analysis Pipeline version=20200220

Description

The main purpose of this pipeline is to achieve 1, circularized hpylori chromosomal; 2; plasmid contigs and base modification calls of m6A, m4C, and potentially m5C; 3, motif summary of pass filter base modifications. It is consisted of 3 aspects.

• Main Pipeline: assuming everything runs smoothly from start to end.
• Reseq Pipeline: For chromosomal contigs that fail to circularise with default circlator run, we will retrieve assemble fasta and run resequence analysis(mapping subreads to assembly) and run a ciruclarization again.
• Plasmid Followup Pipeline: For plasmid contigs that fail to circularise with default run, we will have 3 ways to try to ciruclarize.

Main pipeline:

• Step 01: step1_running_hgap_circlator_batch.sh (to run hgap on demultiplexed samples, for now we don't need to run this one because Kristie is currently running HGAP through SMRTLink)
• Step 02: step2_running_hgap.sh $MANIFEST (to run circlator and nucmer self repeat)
• Step 03: step3_format_hgap_result_batch.sh $MANIFEST (to collect hpylori chr contig and plasmid contig, format them and create ref file for base modification call)
• Step 04: step4_running_basemod_submit.sh $MANIFEST (to run base modification call)
• Step 05: step5_retrieve_stats.sh $MANIFEST (to generate report)
• Step 06: step6_delivery.sh $MANIFEST (to copy deliverables to DataDelivery folder)

Sample Manifest provided by lab(first 3 columns are required): Vial ID CGR ID HGAP Analysis Job ID Demultiplex Barcodes Analysis Job ID PB barcode name demultiplexed data id POR-001 SC489836 2274 2193 BC1001 3237 POR-002 SC489837 2273 2193 BC1002 3238 POR-003 SC489838 2272 2193 BC1004 3233 POR-004 SC489839 2271 2193 BC1008 3239 POR-005 SC489840 2270 2193 BC1009 3234

Reseq Pipeline(force closure of uncircularized chr contig)

Reseq chr cicularization pipeline(snakemake): #intend to run on the sample with chr contig fail to circularize in previous step1_running_hgap_circlator_batch qsub -cwd -q $QUEUE -N ${SAMPLE} -o ${STDOUT} -e {STDERR} -s /bin/sh reseq_pipeline/mainSnake.sh ${SAMPLE} #SAMPLE in the format of POR-005_SC489840_2270

Plasmid cicularization follow up pipeline(snakemake) :

01: to run hgap on plasmid only data with read length filter to remove chimeric expansion sh plasmid_pipeline/submit_main.sh plasmid_pipeline/manifest_example.txt 02: in case of previous step fail to ciruclarize, substitute hgap with canu sh plasmid_pipeline/submit_main_canu.sh plasmid_pipeline/manifest_canu_example.txt 03: in case of both previous steps fail to circularize, pull out all reads mapped to plasmid contig and redo assemble again sh plasmid_pipeline/submit_resequence.sh plasmid_pipeline/manifest_reseq_example.txt