Paul Stothard's repositories
sequence_manipulation_suite
A collection of simple JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. The Sequence Manipulation Suite is commonly used by molecular biologists, for teaching purposes, and for program and algorithm testing.
helpful_commands
Command-line tools, commands, and code snippets for performing routine data processing and bioinformatics tasks.
cgview_comparison_tool
The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, and mitochondrial sequences.
helpful_links
Links to resources related to bioinformatics and data analysis.
ncbi_search
This script uses NCBI's Entrez Programming Utilities to perform searches of NCBI databases. This script can return either the complete database records, or the IDs of the records.
document-builder
Produces nicely formatted PDF and HTML documents from Markdown source files.
genotype_conversion_file_builder
A pipeline for determining the genomic location and transformation rules for the variants described in Illumina or Affymetrix genotype panel manifest files.
sort_markdown_by_headings
Sorts a Markdown file based on headings.
chimeric-mitochondrial-RNA-analysis
Methods and scripts used to characterize chimeric mitochondrial RNA transcripts.
seq_to_json
Converts a raw, FASTA, GenBank, or EMBL file to a JSON file. Feature information is included in the output from GenBank and EMBL files.