pre-process illumina reads
A pretty strongly opinionated, iterative, guided contig assembly pipeline. Integrates spades (+error-correction), bwa-mem, bedtools, and samtools.
Our laboratory repository
software for UCE (and general) phylogenomics
Variety of Code for Counting Illumina Index Sequences
Tally Approximations of Phylogenetic Informativeness Rapidly (TAPIR)
edit distance sequence tags and helpers
Virtual digests of DNA
Software for processing data from RADcap
bioinformatics program recipes for the conda package manager
demultiplex massively parallel sequencing data
parallel, automated SH-testing
An Alfred workflow to interact with a user's Zotero data.
Code for designing UCE probes
the application and database underlying birds.faircloth-lab.org
a cookiecutter template for a protocols package
illumina library prep protocol
Tools for sequence and alignment manipulation
Bayesian haplotype-based polymorphism discovery and genotyping.
An alternative python mechanism to access the Illumina BaseSpace API
Locate, error-correct, trim, and organize (hierarchically) sequence-tagged next-generation DNA reads
Repository of different outgroup databases for use building UCE trees