README.md

In alberto-rodriguezizquierdo/airen_r: A R package to optimize the performance of Restriction digestion to improve the resolution of GBS

airen_r

airen: A R package to optimize the performance of Restriction digestion to improve the resolution of WGS

Requirements:

• R environment (>4.0).
• Reference genome in FASTA file (.fa)
• Genomic aligner (like HISAT2).

Functions and options

In general, the main package is generally adressed to define the best combination of restriction enzymes over a genome in order to increase the resolution of WGS sequencing. The functions of the package are defined by:

• restrictionSimulation: Performance of in-silico restriction enzymes using SimRAD package using our function restrictionSimulation (you have to stablish the range of desired size of fragments, and multiple options are defined to choose your action: 'finding', 'combination' and 'replicate'.

'finding': Use a database of 400 enzyme to predict the best enzyme to obtain the most quantity of fragments in the desired size range from the reference genome. 'combination': Use two chosen enzymes (presents in the airen enzyme database) to perform the in-silico digestion. 'replicate': Use the chosen enzyme(s) to repeat the same in-silico digest in order to predict accurately the number of expected fragments.

• randomGenomeFragmentation: Performance of random genome fragmentation using the reference genome and stablishing the number of repetitions to have a good representation of control data.
• calculatePositionFragment: Function that allows to locate the aligned fragments in the reference genome, in order to identify the cut sites.

Workflow

The main workflow is defined by that steps:

restrictionSimulation function

• Defining the best enzyme to increase the number of expected framgents from a desired range using restrictionSimulation and 'finding' condition.
• Performing the combination of the two best enzymes with the most quantity of desired fragments to show the potential of the combination using 'combination' condition.
• Repeat n times the restriction to increase the accuracy of the prediction using 'replicate condition'.

randomGenomeFragmentation function

• Generate n random genome fragmentation in order to generate a control to compare the efficiency of the restriction enzyme.

Alignment with some aligner like HISAT2 and generate a SAM file.

calculatePositionFragment function

• Identify and compare the control random genome fragmentation to the resulted fragments from the in-silico digestion using the SAM file.

alberto-rodriguezizquierdo/airen_r documentation built on Jan. 29, 2024, 6:27 a.m.