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2014-10-22
This repository contains various scripts and utilities that don't belong to any particular project.
Some of the code is quite useful as is while other code requires additional information to be useful. I'll try to update all pieces of code and example data files so that the code can be tested.
2026-02-16
| Script | Purpose | Category |
|---|---|---|
| Ab1tofastq.py | Use BioPython to convert Sanger sequence files to FASTQ reads | Reuse of barley Sanger data |
| Alchemy_Calls.sh | Bash script to drive Alchemy genotype calls | Barley genotyping datasets |
| FASTQ_dumper.sh | An SRA download script | Reuse of next generation sequence |
| file_rename.py | Bulk renames files programmatically based on a pattern or mapping list. | general_utilities |
| list_unique.py | Parses a file or column and outputs only the unique, non-duplicated entries. | general_utilities |
| getCol2.pl | A quick Perl utility to extract the second column from tabular data. | general_utilities |
| create_Illumina_lookup.py | Generates the lookup dictionaries needed for Illumina SNP microarrays. | SNP_location |
| Illumina_lookup.py | Maps or formats Illumina manifest and array probe data. | SNP_location |
| Illumina_lookup.sh | Maps or formats Illumina manifest and array probe data. | SNP_location |
| GLnexus.sh | Joint genotype calling across multiple gVCFs. | variant_calling |
| Alchemy_Calls.sh | Drives genotype calling using the Alchemy software (useful for legacy array data). | variant_calling |
| paftools_call.sh | Calls variants from PAF alignment formats using Minimap2's paftools. | variant_calling |
| smoove.sh | Runs Smoove (which wraps Lumpy) to call and filter structural variants. | variant_calling |
| sniffles.sh | Identifies structural variants from long-read sequence alignments using Sniffles. | variant_calling |
| svim-asm.sh | Calls structural variants from whole-genome assembly alignments using SVIM-asm. | variant_calling |