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Hurwitz Lab

Login: hurwitzlab

Company: null

Location: Tucson, AZ

email: hurwitzlab@gmail.com

Blog: http://hurwitzlab.org

Members

Repositories

16sblaster: null
abe487-web-tester: null
agave-app-test: Automatic tests for iMicrobe and muSCOPE apps.
agave-file-browser: Agave File Browser
align-consensus-variation: Simple pipeline demoing alignment, consensus generation and variation
amplicon-illumina: null
appetizer: Create the app.json for Stampede
assembly-pipeline: Pipeline to assemble reads into contiguous sequences with MegaHit
assembly-velvet: null
bacteria-bowtie: Simple bioinformatics pipeline to align / count RNA reads to a bacterial genome with bowtie2 / cuffnorm and cuffquant
BioInstaller: BioInstaller can be used to download/install bioinformatics tools, dependences and databases in R relatively easily.
blast-pipeline: null
bowtie: null
bowtie-samtools: Runs bowtie2 and samtools on stampede2, Part two of Radcot
bowtie-to-contigs: A simple pipeline using bowtie to map reads to a co-assembly
centrifuge: Run Centrifuge on Stampede
centrifuge-bubble: Stampede app for creating bubble plots from Centrifuge TSV files
Centrifuge_Bubble: Runs Centrifuge classification on input fasta/q reads and generates a proportional classification bubble plot.
centrifuge-filter: Use Centrifuge calls to filter sequence (FASTA) into accepted/rejected
Centrifuge_HPC: null
centrifuge-patric: Run Centrifuge on Stampede2 and get genomes for downstream applications
commet: Singularity container for COMMET
commet-src: Comparing and combining multiple metagenomic datasets
cuffdiff-keggR: Runs bowtie2 and cufflinks applications on Stampede2 to quantify RNA reads in metagenome samples
cuffdiff-keggR: Runs bowtie2 and cufflinks applications on Stampede2 to quantify RNA reads in metagenome samples
cuffdiff-keggR: Runs bowtie2 and cufflinks applications on Stampede2 to quantify RNA reads in metagenome samples
covstats-with-r: Doing coverage analysis with R
crc-mouse-known-cd-hit: CD-HIT pipeline for 'known' DNA CDS
creakle-host-screen: Creakle uses k-mers to find sequence similarity for screening host reads
cuffdiff-keggR: Runs bowtie2 and cufflinks applications on Stampede2 to quantify RNA reads in metagenome samples
cuffdiff-keggR: Runs bowtie2 and cufflinks applications on Stampede2 to quantify RNA reads in metagenome samples
cuffdiff-keggR: Runs bowtie2 and cufflinks applications on Stampede2 to quantify RNA reads in metagenome samples
cyverse-app-template: A template for CyVerse App development.
cyverse-file-download: Download files into your Cyverse Data Store
d3.chart.bubble-matrix: A bubble-matrix chart based on d3.chart
dada2: Singularity image for R/dada2
dfu-bubble-plots: Repo to generate some figures for the DFU project
Diamond: Utilizes Diamond to generate BlastX data from sequence reads
docker-abyss: null
docker-fizkin: null
docker-glimmer: null
docker-hitman: Dockerized Hitman
docker-idba: null
docker-mash: Docker MASH
docker-metavelvet: null
docker-mga: null
docker-mothur: Docker image for running mothur.
docker-mummer: null
docker-newbler: null
docker-phaccs: null
docker-prodigal: null
docker-refseqmash: Docker version of RefSeqMash
docker-sna: Perform SNA analysis based on R
docker-soap-de-novo: null
docker-spa: null
docker-uproc: null
docker-velvet: null
docker-virsorter: Docker for Virsorter
download-dbgap: Just simple script(s) to download SRA data from dbgap
download-genbank-format: Download *.gbff.gz files from NCBI Reference Genomes
download-patric: Just some simple pbs scripts to download PATRIC data (bacterial genomes and metadata)
download-tcga: Scripts to download / manipulate TCGA data from GDC
elm-imicrobe-search: null
elm-imicrobe-spa: null
extract-fasta: Use bedtools to extract fasta that is annotated with a gff file
fizkin: All-vs-all sequence comparison for WGS
imicrobe-admin-console: A Flask-Admin interface to the iMicrobe database.
imicrobe-admin-console: A Flask-Admin interface to the iMicrobe database.
foundation-python: Testing out job submission with Python
funannotate: Stampede2 implementation of https://github.com/nextgenusfs/funannotate
gnu-parallel-yourself: Template script and instructions for using GNU Parallel in place of the TACC Launcher on Stampede2.
graftm: graftM Singularity for Stampede2
haskell: null
hello-singularity: Demonstrate building a Singularity container.
Host-Screen: Utilizes Bowtie2 to remove host contaminated read from Fasta/q files
hpc-prodigal: HPC code to run Prodigal on PBS
hpc-virsorter: PBS implementation of VirSorter
imicrobe-16SrDNA-OTU-Clustering: A CyVerse pipeline for clustering 16S rDNA data.
imicrobe-ABySS: null
imicrobe-admin-console: A Flask-Admin interface to the iMicrobe database.
imicrobe-admin-console: A Flask-Admin interface to the iMicrobe database.
imicrobe-annotdb: iMicrobe sample annotation database
imicrobe-blast: null
imicrobe-data-loaders: Scripts to load UProC results into the iMicrobe database.
imicrobe-IDBA: null
imicrobe-landing-page: Static HTML/CSS for iMicrobe landing page
imicrobe-lib: General purpose scripts and libraries for iMicrobe.
imicrobe-mash: null
imicrobe-mash-node2vec: Scripts to learn and cluster a vector-space embedding on all-vs-all iMicrobe MASH distance matrix.
imicrobe-MegaHit: A CyVerse app for running the MegaHit assembler.
imicrobe-metaSPAdes: null
imicrobe-MetaVelvet: null
imicrobe-misc: Miscellaneous script for iMicrobe.
imicrobe-mixs: null
imicrobe-mojo: Mojolicious web server for iMicrobe data site.
imicrobe-prokka: A CyVerse app to run Prokka.
imicrobe-puca: A sneaky app.
imicrobe-SOAPdenovo2: null
imicrobe-test: Automated tests for the iMicrobe website.
imicrobe-vm: Scripts to provision a VM to run iMicrobe.
infant_diabetes: Pipeline for analysis of "A prospective, longitudinal analysis of the developing gut microbiome in infants en route to type 1 diabetes"
interpro: Singularity/Stampede2 InterPro
iPlant-Bonnie: Scripts to run Bonnie's pipeline on iPlant/Stampede
isogenie-assemblies: Isogenie assembly work
isogenie-permafrost: Isogenie work on permafrost scripts
its: null
ivirus-lib: iVirus general code
ivirus-mojo: Mojo for iVirus
Jellyfish: A fast multi-threaded k-mer counter
jellyfish-query-haskell: null
karect: Karect for Stampede2
kmerizer: Working with k-mers
kmer-sge: Original code for k-mer/SNA analysis using SGE (Hurwitz et. al. PNAS)
kogiri-spark: null
Krona: Interactively explore metagenomes and more from a web browser.
launcher: A simple utility for executing multiple sequential or multi-threaded applications in a single multi-node batch job
launch-yourself: Template script and instructions for using the TACC Launcher on Stampede.
LSA-pipeline: LatentStrainAnalysis to separate out fastas into genome bins which can then be assembled individually
make-custom-patric-metagenome: Takes a list of genomic ids (patric format) and ultimately gives you a fasta with all the fetched genomes
make_pretty_bar_graphs_in_R: R script to make some good-looking bar graphs
mash: null
mash-on-patric: Running mash on patric to collapse strains into tighter species groupings
mds.js: Classic Multidimensional scaling code in Javascript
megahit: Stampede implementation of MEGAHIT
meowl: Microbial Environments described using OWL (MEOWL)
metapalette: Singularity/Stampede app
mg-sample-data: Sample data for a metagenomic / metatranscriptomic workflow
mixs-ui: UI for entering MIxS
ML_Feature_Extraction_TRAINING: pipeline for features extraction (kmer frequency count) to train a linear classifier
MR-PKM: Hadoop MapReduce implementation of Pairwise K-mer Mode pipeline for metagenomics
muscope-18SV4: A CyVerse app implementing "Microbial eukaryotic 18S tag-sequence processing/QC - V4 region" from protocols.io.
muscope-admin-console: A Flask-Admin interface to the muSCOPE database.
muscope-blast: null
muscope-data-loaders: Load and validate muSCOPE data.
muscope-last: LAST for muSCOPE.org
muscope-lib: Libraries, data models, scripts for muSCOPE
muscope-mash: null
muscope-mojo: Mojolicious for muSCOPE
ncbi-genome-download: Scripts to download genomes from the NCBI FTP servers
NeutropenicFever: Scripts for FN analysis
NF_Data_and_Scripts: null
node2vec: Fork of node2vec to provide Python 3 support.
node-imicrobe: Node app server for iMicrobe data
occ-plan-b: Hadoop job service
ohana: Ohana gene catalog work
orminator: Generate SQLAlchemy ORM classes for an existing database.
patric-curation: A pipeline to curate the PATRIC database for phages and other necessary tasks
pave: PaVE
pcpipe: null
pear: null
perl-lib: Perl utilities
PhiSpy: null
PHYling_unified: Stampede implementation of PHYling_unified
prodigal: null
prokka: Fork of :zap: :aquarius: rapid prokaryotic genome annotation to add --notbl2asn
ProphET: null
public-protocols: null
qc: QC scripts
Radcot: Determines bacterial genomes from DNA reads then shows gene expression differences from RNA reads
readabundance_fastbit: null
refseq-mash: MinHash RefSeq for species discovery
RNA_qc: Simple pipeline to QC RNA and then sort and merge fastq files to be properly paired
robotframework-jsonlibrary: Robotframework Test Library to manipulate JSON using JSONPath
saffrontree: Stampede2 SaffronTree
SARTools: Statistical Analysis of RNA-Seq Tools
simka: Singularity/Stampede app
simple_venn: Uses R to make a venn diagram of two data frames
sim-plots: Sequence similarity plots in D3
singularity-bbtools: Singularity container for bbtools (https://jgi.doe.gov/data-and-tools/bbtools)
singularity-bowcuff: Bowtie2 - Samtools - Cufflinks in one singularity image
singularity-centrifuge: null
singularity-fastqc: A singularity image for doing quality control on DNA / RNA fastq files
singularity-fizkin: Singularity container for Fizkin
singularity-graftM: Singularity image of https://github.com/geronimp/graftM
singularity-kronatools: Scripts to make a singularity container for krona taxonomy tools
singularity-patric-cli: A singularity image for patric-cli https://docs.patricbrc.org/cli_tutorial/index.html
singularity-phispy: Singularity container for phispy
singularity-prophET: Singularity container for prophET (https://github.com/jaumlrc/ProphET)
singularity-python-faves: Scott's favorite pythonic bioinformatic tools / scripts (and possible a few others :) )
singularity-taxoner: Singularity image for running taxoner and bowtie2 on a combined DNA / RNA dataset for bacterial metagenomics
cuffdiff-keggR: Runs bowtie2 and cufflinks applications on Stampede2 to quantify RNA reads in metagenome samples
cuffdiff-keggR: Runs bowtie2 and cufflinks applications on Stampede2 to quantify RNA reads in metagenome samples
cuffdiff-keggR: Runs bowtie2 and cufflinks applications on Stampede2 to quantify RNA reads in metagenome samples
soong-lib: null
stampede2-template: Template for creating pipelines on TACC stampede cluster.
stampede2-template: Template for creating pipelines on TACC stampede cluster.
stampede-cdhit: Stampede implementation of cd-hit
stampede-clark: Stampede implementation of CLARK
stampede-creakle: Scripts to get Creakle host screen to run on TACC/stampede.
stampede-fizkin: Fizkin/Singularity for TACC/stampede
stampede-idba: Stampede implementation of IDBA assembler
stampede-pcpipe: PCPipe for TACC stampede.
stampede-spades: Stampede implementation of SPAdes
stampede2-template: Template for creating pipelines on TACC stampede cluster.
stampede2-template: Template for creating pipelines on TACC stampede cluster.
stampede-velvet: Stampede implementation of velvet assembler
stampede-virsorter: Implementation of VirSorter to run in parallel on TACC stampede.
tacc-apps: null
tacc-fizkin: null
tacc-launcher-example: Example of using the TACC Launcher
taxoner: null
taxoner-patric: Uses taxoner64 and PATRIC bacterial database to map fastq/fasta to genomes
test1-68fcf1fe-c194-4f2b-9c17-e23e65b54298-bhurwitz33: test1-68fcf1fe-c194-4f2b-9c17-e23e65b54298-bhurwitz33 created by Classroom for GitHub
trim-galore: Biocontainer Trim Galore for Stampede2
upload-to-de: Just a simple, reusable script(s) to rsync data to cyverses' discovery environment (DE)
uproc: null
uproc-on-anvio: Runs uproc on anvio to ultimately produce a readout of functional enrichment
viral-learning: Deep learning demonstration code.
VirSorter-Euk: Source code of the VirSorter App, available on CyVerse (https://de.iplantcollaborative.org/de/)
virsorter-singularity: Singularity container for VirSorter to run on stampede2

This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.