Welcome to arraylib’s documentation!

arraylib-solve is a tool to deconvolve combinatorially pooled arrayed random mutagenesis libraries (e.g. by transposon mutagenesis). In a typical experiment generating arrayed mutagenesis libraries, first a pooled version of the library is created and arrayed on a grid of well plates. To infer the identities of each mutant on the well plate, wells are pooled in combinatorial manner such that each mutant appears in a unique combination of pools. The pools are then sequenced using NGS and sequenced reads are stored in individual fastq files per pool. arraylib-solve deconvolves the pools and returns summaries stating the identity and location of each mutant on the original well grid. The package is based on the approach described in [BSA+16].

API:

• LibraryExperiment

Tutorials:

• Installation
• How to run simulations with arraylib before arraying a pooled library
• Estimate size of arrayed library to reach a certain number of unique mutants
  • Run interactively
  • Run on command line
• Estimate accuracy of library deconvolution
  • Run interactively
  • Run on command line
• How to run arraylib interactively
  • Read trimming and genomic alignment
  • Assembly of count matrix and preprocessing
  • Deconvolution and location inference
  • References
• How to run arraylib on the command line
  • Input parameters
  • Run only on barcodes
  • Output
  • References

BSA+16

Michael Baym, Lev Shaket, Isao A Anzai, Oluwakemi Adesina, and Buz Barstow. Rapid construction of a whole-genome transposon insertion collection for shewanella oneidensis by knockout sudoku. Nature communications, 7(1):13270, 2016.