nick-youngblut/snakemakeNB

This repository has been archived on 05/Jan/2020
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Jupyter Notebook
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MIT License
Created almost 8 years ago
Updated almost 8 years ago

nick-youngblut/snakemakeNB

nick-youngblut

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Create snakemake rules to run Jupyter/Ipython Notebooks

gtdb_to_taxdump

Convert GTDB taxonomy to NCBI taxdump format

traitar3

From genomes to phenotypes: Traitar3, the microbial trait analyzer (for Python3)

MGSIM

Metagenome read simulation of multiple synthetic communities

MFEprimer_linux

A fast thermodynamics-based program for checking PCR primer specificity (setup.py: linux install)

CLdb

Create a local pan-genome CRISPR database

pushmsg

IPython magic function to send notifications with Pushbullet

seqDB_tools

commands for interacting with public sequence databases

Tax4Fun

unofficial Tax4Fun repo

pop_genome

Population genomics scripts - many build upon ITEP

tree_edit

tools for manipulating phylogenies

sgepy

SGE job submission & monitoring

misc_perl

miscellaneous perl scripts that haven't yet been migrate to another repo

gtl_read_filter_pipeline

Illumina read filtering pipeline for the GTL project

seq_tools

Miscellaneous tools for working with sequences

HTSSIP

An R package for analyzing high throughput sequence stable isotope probing data

FORAGer

Finding Orthologous Reads and Genes

metagenome_assembly

Various scripts for metagenome assembly

consenTRAIT

Phylogenetic conservatism of functional traits in microorganisms

SIPSim

A toolset for simulating high resolution stable isotope probing data

Jupyter Notebook