pbAmp-seek 🔬
Identify and count PacBio Hifi amplicons
This is the home of the pipeline, pbAmp-seek. Its long-term goals: to identify and count PacBio Hifi amplicons like no pipeline before!
Overview¶
Welcome to pbAmp-seek's documentation! This guide is the main source of documentation for users that are getting started with the long pipeline name.
The ./pbAmp-seek pipeline is composed several inter-related sub commands to setup and run the pipeline across different systems. Each of the available sub commands perform different functions:
pbAmp-seek run: Run the pbAmp-seek pipeline with your input files.pbAmp-seek unlock: Unlocks a previous runs output directory.pbAmp-seek cache: Cache remote resources locally, coming soon!
pbAmp-seek is a comprehensive pipeline to identify and count PacBio amplicons. It relies on technologies like Singularity1 to maintain the highest-level of reproducibility. The pipeline consists of a series of data processing and quality-control steps orchestrated by Snakemake2, a flexible and scalable workflow management system, to submit jobs to a cluster.
The pipeline is compatible with PacBio hifi reads. In brief, the hifi reads will be clustered to find consensus sequences (amplicon sequences) with pbAA (https://github.com/PacificBiosciences/pbAA) using the provided reference sequences as guides. The consensus sequences will then be aligned to the reference for comparison. The hifi reads will also be aligned to the consensus sequences to quantify their relative proportion in the pool. Alignment is performed with pbmm2 (https://github.com/PacificBiosciences/pbmm2). In the end, a summary file ({sample}_summary.csv) will be generated to report what consensus sequences were found, where they aligned to the reference, and how many reads were mapped to them (in both absolute and proportional values). Detailed reference-consensus alignment information is also provided in bam, mpileup, and vcf files.
As input, it accepts a set of FastQ files and can be run locally on a compute instance or on-premise using a cluster. A user can define the method or mode of execution. The pipeline can submit jobs to a cluster using a job scheduler like SLURM (more coming soon!). A hybrid approach ensures the pipeline is accessible to all users.
Before getting started, we highly recommend reading through the usage section of each available sub command.
For more information about issues or trouble-shooting a problem, please checkout our FAQ prior to opening an issue on Github.
Contribute¶
This site is a living document, created for and by members like you. pbAmp-seek is maintained by the members of NCBR and is improved by continous feedback! We encourage you to contribute new content and make improvements to existing content via pull request to our GitHub repository .
References¶
1. Kurtzer GM, Sochat V, Bauer MW (2017). Singularity: Scientific containers for mobility of compute. PLoS ONE 12(5): e0177459.
2. Koster, J. and S. Rahmann (2018). "Snakemake-a scalable bioinformatics workflow engine." Bioinformatics 34(20): 3600.