Thomas Sharpton's repositories
meta-qc
A QC pipeline for shotgun metagenomic data derived from host-associated microbial communities (i.e., microbiomes)
MicrobeDB
Provides a local database of in-house and published genomes for Bacteria and Archaea from NCBI
quickclass
Conducts a quick and dirty classification of DNA sequences into protein families. Takes demultiplexed Illumina fastq data, organizes it into sample categories, pushes the data to an SGE cluster, process it with LAST using a precomputed protein family database, and parses the result to identify the number of copies of each family in each sample.
seq-scripts
scripts sequence and feature conversion, annotation, analysis ...
Sfam_updater
Code and versioning notes for the Sfams protein families.
shotcleaner
A high-throughput and modular workflow to quality control shotgun metagenomic DNA sequence libraries