Bacterial genome annotation script using BLASTN v2

This protocol uses a python based script and command-line BLASTn to annotate in a final table single-read sequencing results from genome amplifications, within other output files. Its main use in our lab (https://biocomputationlab.com) is to identify the location and gene locus of transposon inserts in microbial bacterial genomes of Pseudomonas putida KT2440. However, this script can be used for other bacterial genomes for which its genome sequence and annotation are available. Script was developed and tested in python 3.11.9 with blastn version 2.9.0, sickle version 1.33 and fastqc version 0.11.9 This is a description of the LAP entry LAPu-InsertsGenAnnotation-2.0.0 located in the LAP repository, specifically LAPu-InsertsGenAnnotation-2.0.0 and Github Entry LAPu-InsertsGenAnnotation-2.0.0, 2 places that you can download directly the script used and usage examples The major changes from previous version are: File format for -identity Argument: Now accepts XLSX and CSV files. New Argument --summaryMap: Added the --summaryMap argument. Enhanced -quality Argument: When provided, the merged quality file (FastQC file) will use the file name (without extension) as the sequence identifier, which will match the qaccver in the table_reads_gene_description.csv file. Support for Numeric Identifiers: Numeric identifiers follow the same rules as well names for locating them in a file or sequence identifier. Identifier Pattern for Sequences: The script recognizes the last element of the pattern (+well_, +number_, _well_, _number_) as the sequence identifier for -identity and --summaryMap arguments. More read extensions accepted: they will be treated as previously txt files are treated for all other arguments