phiXXer

phiXXer: Assemble fosmid inserts from nanopore sequencing of phiX amplified products

Installation

One-time setup: Create a conda environment phiXXer_env by running sh.install_phiXXer_env.sh

Running the pipeline

For each new run, the qsub script job-phiXXer.v0.0.sh needs to be edited as follows:

1. Prepare and provide a tab-separated file which should have two columns: (1) the nanopore_barcode_numnber, and (2) user-specified fosmid_clone_ID. This filepath should be provided to as the value for the variable input_metadata in the qsub script.
2. Update all other User-specified parameters (lines 25 to 32) in the qsub script.
3. As of now, 96 samples can be multiplexed using nanopore barcodes. The corresponding data can be analyzed in paralled on SGE by specifying -t 1-96 (line 10) in this qsub script.
4. Submit the job via qsub

Citing phiXXer

The complete experimental and computational workflows are described in the following research article:

• Chuzel, L., Sinha, A., Cunningham, C. V., and Taron, C. H. (2024). High-throughput nanopore DNA sequencing of large insert fosmid clones directly from bacterial colonies. Applied and Environmental Microbiology 90, e00243-24. doi:10.1128/aem.00243-24.