Joseph7e

Assess-NCBI-sequence-availability

This repository contains scripts and bioinformatics workflows for various use cases of the NCBI taxonomy database and the collection of various sequence databases.

Assign-Taxonomy-with-BLAST

Assign taxonomy with blast, can be used for qiime

Bioinformatic-Tutorials

This is a table of contents to the Hubbard Center for Genome Studies bioinformatic tutorials and resources.

Coronavirus-Bioinformatic-Exercises

HCGS-BASH-tutorial

Getting started on a server

HCGS-Comparative-Genomics

NCBI download and Orthofinder analysis

HCGS_Metabarcoding_Tutorials

Workflow for qiime2 workshop

MAKER-genome-annotations-tutorial

Construct ab initio gene prediction using only BUSCO augustus models. Add in transcriptome for extra support

MDIBL-T3-WGS-Tutorial

Bacterial Genome Assembly and Assessment

Nanopore-Workflow

Working pipeline for nanopore + illumina data

Joseph7e/MDIBL-T3-WGS-Tutorial

Bacterial Genome Assembly and Assessment

Joseph7e/Assign-Taxonomy-with-BLAST

Assign taxonomy with blast, can be used for qiime

Joseph7e/MAKER-genome-annotations-tutorial

Construct ab initio gene prediction using only BUSCO augustus models. Add in transcriptome for extra support

Joseph7e/HCGS_Metabarcoding_Tutorials

Workflow for qiime2 workshop

Joseph7e/HCGS-Comparative-Genomics

NCBI download and Orthofinder analysis

Joseph7e/Nanopore-Workflow

Working pipeline for nanopore + illumina data

Joseph7e/Bioinformatic-Tutorials

This is a table of contents to the Hubbard Center for Genome Studies bioinformatic tutorials and resources.

Joseph7e/HCGS-BASH-tutorial

Getting started on a server

Joseph7e/Assess-NCBI-sequence-availability

This repository contains scripts and bioinformatics workflows for various use cases of the NCBI taxonomy database and the collection of various sequence databases.

Joseph7e/Coronavirus-Bioinformatic-Exercises

Joseph7e/Island-Finder-Scripts

Joseph7e/Marker-genes-as-predictors-of-shared-genomic-function

Scripts and data for Sevigny et al. 2018. Marker genes as predictors of shared genomic function.

Joseph7e/MDIBL-T3-WGS-Comparative

Joseph7e/Genome-Sequencing-and-Comparative-Genomic-Analysis

NIGMS cloud module development for comparative genomic analysis

Joseph7e/HCGS-Genomics-Tutorial

Joseph7e/Meiofauna-Phylogeography

Git to hold complete scripts and files related to graduate research

Joseph7e/seqtk

Toolkit for processing sequences in FASTA/Q formats

Joseph7e/summarize-snps-with-gff

Joseph7e/Biodiversity-estimates-and-ecological-interpretations-of-meiofaunal-communities

Repository to house code for Leasi et al. 2018

Joseph7e/BITMaB2-Tutorials

Joseph7e/genetic-relatedness

HTML for genetic relatedness lesson with PLINK

Joseph7e/Joseph7e

Personal and Professional Website - Joseph L. Sevigny

Joseph7e/Mitobin

Scripts and data for the mitobin program

Joseph7e/Nematode-Mitochondrial-Metagenomics

scripts and data for the analyses in the manuscript - Nematode Mitochondrial Metagenomics – a New Tool for Biodiversity Analysis

Joseph7e/NG-MMAT

Joseph7e/NGMSAT

Program to identify primers and repeat counts from Illumina FASTQs - targeting microsatellite loci

Joseph7e/Pathogen-Identification

Joseph7e/Primer-Extract

Results and Methods for in silico extraction of amplicon fragment given a set of primers and distance comparison of two primers

Joseph7e/Target-Enrichment-of-Metazoan-Mitochondrial-DNA-with-Hybridization-Capture-Probes

code and tutorials for data analyses related to the manuscript submitted to Ecological Indicators

Joseph7e/Tick-Surveillance

Bioinformatic workflows and tools for DNA sequencing analysis of tick species.