Ed Davis's repositories
get_assemblies
Download assembly files from NCBI
automlsa2-examples
Example datasets for automlsa2 script.
moore-2021-acetone
Acetone monooxygenase (SAR11_0845) homolog analysis using Tara metatranscriptome data
AGAT
Another Gtf/Gff Analysis Toolkit
alv
A console-based alignment viewer
bakta
Rapid & standardized annotation of bacterial genomes & plasmids
BASTA
Basic Sequence Taxonomy Annotator
Bracken
Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
btop
A monitor of resources
clinker
Gene cluster comparison figure generator
davis-2022-ZAM
Analysis for the Davis et al 2022 PLOS ZAM study.
drep
Rapid comparison and dereplication of genomes
FAMSA
Algorithm for ultra-scale multiple sequence alignments (3M protein sequences in 5 minutes and 24 GB of RAM)
funannotate
Eukaryotic Genome Annotation Pipeline
git-cheat-sheet
:octocat: git and git flow cheat sheet
HBH-2021
Hypoxic barrier hypothesis manuscript data analysis
MITObim
MITObim - mitochondrial baiting and iterative mapping
primerclip
Swift Accel-Amplicon primer trimming tool for fast alignment-based primer trimming
qrcode.show
[WORKING PROTOTYPE] Generate QR code easily for free - QR Code Generation as a Service
r-pilot
A minimal ggplot2 theme with an accessible discrete color palette.
rich
Rich is a Python library for rich text and beautiful formatting in the terminal.
SequenceBouncer
A Python3 script for removal of outlier sequences from a multiple sequence alignment (FASTA format).
spack
A flexible package manager that supports multiple versions, configurations, platforms, and compilers.
starcli
:sparkles: Browse trending GitHub projects from your command line
vire
Vim / Neovim installer and vimrc + plugin manager