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194_bouru_shotgun_analysis

amplicon_workflows

Workflows and scripts for amplicon sequencing processing

bactpipe

BACTpipe: An assembly and annotation pipeline for bacterial genomics

bioinformatics_curriculum

Some ideas on things to learn to get started with bioinformatics

bvab-and-lac-sequences

The database contains a collection of sequences for BVAB (Bacterial vaginosis associated bacteria) and common vaginal Lactobacillus species.

claritylims

Customizations for our GenoLogics BaseSpace Clarity LIMS

crc-survival

Code for Tumor Microbiome is associated with survival in late stage colorectal cancer

ctmr-superset

Custom Docker image for Apache Superset

ctmr_lab_interface

Scripts used to facilitate the interface between bioinformatic and experimental microbiology

dockerfiles

Dockerfiles used at CTMR

ena_submission_notebooks

Notebooks in Jupyter that can be used for filling out meta data checklists required for uploading data to the ENA

estimate_seq_depth

A small workflow that simulates metagenomes for use in estimating the required sequencing depth for different type of microbiome samples

estimate_seq_depth_notebooks

Notebooks for the estimate_seq_depth project

gitdemo

list_scanner

List scanning application

mgi-ncov19-snakemake

optivag

Database for annotating vaginal communities

print_ctmr_labels

Print CTMR labels on Zebra printer

pseudomonas_boanensis_db1

comparative genomic analysis for Pseudomonas boanensis DB1

rstudio_singularity

Run Rstudio with Singularity

run_in_parallel

Run simple commands in parallel on Slurm

s3etag

Compute ETag of local file and compare to file on S3

salgae_c-di-gmp_analysis

Minhash/pangenome analysis notebooks and associated files

sars-cov-2_multi-pcr_v1.0

SARS-CoV-2 analysis pipeline for multiplex-PCR MPS(Massive Parrallel Sequencing) data

slurm-jobstats

Compute job statistics for Slurm jobs

sm3

Simple Snakemake example

sourmash_sketch

Compare samples based on kmers using Sourmash sketch

stag-mwc

StaG Metagenomic Workflow Collaboration

valody

A tool to assign VAginaL DYnamic categories to individuals based on their Valencia CST assignments

zebra_gk420t

Script for printing labels on Zebra GK420t