ig_genes_ferret

A detailed workflow of how I (and colleagues) predicted Mustela mutorius furo (the domestic ferret) immunoglobulin (Ig) genes using the ferret genome assembly ASM1176430v1.1 and then mapped ferret B cell receptor sequencing data to those predictions.

Table of contents

• variable_gene_prediction/: A directory containing all scripts used in the prediction of ferret variable region Ig genes (i.e. IGHV, IGHD, IGHJ, IGKV, IGKJ, IGLV, IGLJ gene segments) and a description of how they were used. These scripts are generalizable to the discovery of Ig genes in other species, though some customization is likely necessary.

• variable_gene_transcript_analysis/ A directory containing all scripts used to analyze B cell receptor variable domain-encoding mRNA (cDNA) transcription data from ferrets, and a description of how they were used. This analysis uses the gene sequences obtained with scripts from the "variable_gene_prediction/" directory.

• constant_gene_transcript_analysis/ A directory containing all scripts used to analyze B cell receptor constant domain-encoding mRNA (cDNA) transcription data from ferrets, and a description of how they were used.

Dependencies

Python packages

All python dependencies are listed in the environment.yml file.

Other tools

Non-python package bioinformatics tools called by the scripts in this repository include:

• BLAST+ suite (version 2.15.0)
• Digger (version 0.7.3)
• IgBLAST (version 1.21.0)
• Cutadapt (version 4.6)
• PEAR (version 0.9.11)
• SignalP (version 5.0b)