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atlas-wrapper

A wrapper to run ATLAS within a Docker container

atm

backblast2

backblast_reciprocal_blast

This repository contains a reciprocal BLAST program for filtering down BLAST results to best bidirectional hits. It also contains a toolkit for finding and visualizing BLAST hits for gene clusters within multiple bacterial genomes.

bioid

A Python package for autonomously identifying Bioinformatic file formats.

bioinformatics_scripts

Scripts UBC

biomagick

A next generation bioinformatics file format converter.

blast-mapper

An iPython notebook containing code for plotting BLAST hit position across multiple genomes using the Bokeh plotting library.

cdhittofasta

Extracts CD-Hit clusters which contain reference proteins and stores them in FASTA format.

comp4530_hello_world

diamond

Accelerated BLAST compatible local sequence aligner.

fraggenescanplusplus

Scalable high-throughput short-read open reading frame prediction

gc_size_select

Visualization of genomic sequencing size selection protocol's influence on per fragment GC content.

genbank-downloaders

A series of small Biopython scripts for downloading sequence data off NCBI's Genbank.

hello-world

Just another repository

hmmer-db

A program for searching, extracting and storing protein sequences that match specific Hidden Markov Models created by HMMER.

homebrew-bio

:beer::microscope: Bioinformatics formulae for the Homebrew package manager (macOS and Linux)

homebrew-fraggenescanplusplus

Homebrew formula for FragGeneScanPlusPlus

homebrew-science

:microscope: Scientific formulae for the Homebrew package manager

hydrophobicity

Online visualization of amino acid hydrophobicity:

interleave-fastq

interleaves fastq files (also gzipped ones!)

jupyter-sqlalchemy-tutorial

Introductory interactive Jupyter tutorial providing details about ORMs in order to assist in the teaching of their use to computing science students.

lee-bergstrand-msc-thesis

Lee Bergstrand's MSc. Thesis

mesas

Microbial Ecology Scripts and Stuff

ncbi_tools

An Unofficial Mirror of NCBI Tools: The ToolBox model and code is used extensively within NCBI for the internal pipelines and tools such as GenBank, Entrez, BLAST, Sequin, OMIM, RefSeq, and others.

ncbiconnect

JavaScript library for interfacing with National Center for Biotechnology Information's databases

phylogenetic-tree-building

A tool kit for extracting 16S rRNA genes from genomes for the purpose of building phylogenetic trees.

shovel

Tools for working with the SPAdes Genome Assembler

st-project

stevelyall.github.io