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Scripts

This repo contains scripts, protocols, and workflows for computational analyses.

Table of Contents

16S_sequence_processing

mothur workflow for our 16S time series data. This workflow is designed to start with a BIOM table and .fasta file of unique sequences.

  • 16S_deblurred_table_mothur_workflow.docs - Instructions for running the BIOM table through mothur and explanation of commands and scripts used
  • names_from_shared.R - Creates a .names file from a .shared file
  • remove_seqs_from_shared.R - If sequences have been removed from the .names file, this script will also remove these from the .shared file
  • `shared_to_count.R'- Converts .shared file to a .count file

KBase

Scripts for batch generation of genome-scale metabolic models using KBase.

  • ModelBuilding - Instructions for batch generation of genome-scale metabolic models using KBase.
  • loadGenomes.pl - Perl script for pushing local genomes to KBase.

MetaPathways

Information pertaining to installation of MetaPathways and for building PGDBs using MetaPathways and PathwayTools.

  • MetaPathwaysInstallation.md - Instructions for installing MetaPathways on the server.
  • MetaPathwaysProtocol.md - Protocol for building a PGDB
  • Config and Param files - configuration and parameter files for running MetaPathways locally and on the server.

OrthoMCL

Scripts for building ortholog groups from proteomes, using OrthoMCL. Also contains a stand-alone script which runs all-vs-all BLAST jobs on multiple processors.

Phylogeny

Scripts for building phylogenetic trees. Currently only contains scripts for building tree using Phylosift marker genes.