Welcome! This repository contains general scripts used throughout the projects at the Kwantlen Polytechnic University Applied Genomics Centre. Scripts are organized into directories based on their function. A brief description of each script is listed below.
Additionally, the wiki contains documentation for each of the scripts as well as general procedures and guidelines for maintaining the bioinformatics resources of the lab.
Scripts and documents related to the use of NCBI BLAST+ 2.12.0.
| Script | Description |
|---|---|
| blast_commands.txt | contains commonly used commands when working with the NCBI BLAST+ 2.12.0 program |
| generate_taxid_map.py | generate a taxid file from Genbank file containing all sequences of interest |
| process_genbank_db.py | generate both a .fasta file containing all sequences in Genbank file, as well as a metadata .csv file |
Examples of how we use common Python modules and documentation templates.
| Script | Description |
|---|---|
| argparse_example.py | contains example implementation of argparse |
| docstrings_example.py | contains example docstring formats for our scripts |
| pathlib_example.py | contains commonly used code when working with pathlib module |
| slurm_scheduler_example.sh | contains example of slurm scheduler script |
| template.py | template of our Python scripts |
Miscellaneous scripts for dealing with common file types.
| Script | Description |
|---|---|
| batch_rename.py | used to sanitize SeqStudio ab1 file names to fit the formats required for our scripts |
| batch_reverse_complement.py | generate reverse complements of several sequences |
| convert_gb_fasta.py | extract .fasta sequences from Genbank files |
| generate_sequence.py | in-silico generation of random DNA sequences |
| calc_ta.py | calculate melting temperatures of several primer sets |
Scripts related to working with SeqStudio ab1 files.
| Script | Description |
|---|---|
| sanger_qc.py | automated QC of Sanger sequences |
| sanger_sequence_trim.py | automated trimming of Sanger sequences (SeqStudio ab1 files) |
| generate_seqstudio_qc.py | generate SeqStudio QC .csv file from solely the ab1 files (used if the original QC .csv is lost) |
Scripts related to sequence analysis tasks.
| Script | Description |
|---|---|
| species_aligner_analysis.py | from a Genbank file containing multiple entries, generate alignments for each species within the GenBank file. |