Skip to content

Science Tutorials with CyVerse

Bioinformatics Tutorials Using CyVerse

Tutorial Date Notes
RNASeq using VICE Dec 06, 2019 Perform RNAseq differential expression analysis using Read Mapping and Transcript Assembly (RMTA) and Rstudio-DESEq2 apps
Assemble a Genome Using SOAPdenovo Dec 19, 2019 Commonly used procedure for de novo whole genome assembly of Illumina reads using the DE: Assemble reads, Assess assembly
Cluster Orthologs and Paralogs and Assemble Custom Gene Sets Dec 11, 2019 Input entire protein-encoding gene or transcript repertoires from genomes of interest, and cluster homologs (orthologs and paralogs), then query clusters to assemble gene sets based on presence/absence and copy number.
RNA-Seq with Kallisto and Sleuth Nov 04, 2019 Kallisto is a quick, highly-efficient software for quantifying transcript abundances in an RNA-Seq experiment. Sleuth is designed to analyze and visualize the Kallisto results in R.
Kallisto-0.42.3-INDEX-QUANT-PE Oct 25, 2019 Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.
Genome Annotation with MAKER Oct 09, 2019 This tutorial is a step-by-step guide for using SciApps to perform MAKER based annotation
Evaluate and Pre-Process Sequencing Reads Jan 05, 2018 Clean and filter Illumina reads using DE apps.
Taxonomic Name Resolution Service (TNRS) Dec 05, 2017 Become familiar with TNRS to identify, correct, and update scientific names of plants.
Submit High-throughput Sequencing Reads to NCBI Sequence Read Archive (SRA) Dec 04, 2017 The SRA is a canonical repository for sequencing data generated by high-throughput instruments. The CyVerse submission pipeline allows you to directly submit your data into an SRA-linked BioProject.
Evaluate High-throughput Sequencing Reads with FastQC Aug 01, 2017 FastQC is a popular tool for evaluating the quality of high-throughput sequencing reads such as from Illumina and PacBio.
HTSeqQC Aug 01, 2017 An automated quality control analysis tool for a single and paired-end high-throughput sequencing data (HTS) generated from Illumina sequencing platforms
Import data from NCBI SRA using the Discovery Environment Apr 04, 2017 The NCBI Sequence Read Archive (SRA) is a repository for high-throughput sequencing reads. These are valuable data for novel analysis and reuse. You can directly import data from SRA into your Data Store using a Discovery Environment app.
Discover Variants Using SAM Tools Oct 11, 2016 Detect and call variants from sequence reads using Bowtie and SAM Tools.
Filter, Trim, and Process High-throughput Sequencing Reads with Trimmomatic Sep 15, 2016 Trimmomatic is a popular application for filtering and trimming high- throughput sequencing reads. Several functions can remove populations of low quality reads, remove sequencing adaptors, and trim low-quality regions of individual reads.
Characterizing Differential Expression With RNA-Seq (Without Reference Genome) Jul 21, 2015 Identify changes in gene expression levels between at least two sequenced transcriptome samples (18 separate tutorials)
BLAST a Transcriptome May 11, 2016 Reduce number of transcripts and level of redundancy in an assembled transcriptome, and identify coding sequences that can be submitted to BLASTP searches.
QIIME-1.9.1 for the DE Apr 12, 2016 QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data.
mini SOAPdenovo Jan 04, 2016 Gain familiarity with a commonly used procedure for de novo whole genome assembly of Illumina reads using the DE.
Genome-wide Association Study (GWAS) Using a Genotyping-by-sequencing Approach Sep 27, 2012 Learn to identify genetic variants that are associated with a trait.

SciApps

Tutorial Date Notes
Association analysis with mixed models Sep 18, 2013 A genome-wide association study (or GWAS) workflow using TASSEL, EMMAX, and MLMM for mixed model analysis.

Atmosphere

Tutorial Date Notes
Basic Stacks Nov 06, 2017 Use next generation sequence data produced from Reduced Representation Libraries (RRL) such as Restriction site associated (RAD) tags.
fastStructure Oct 01, 2017 fastStructure is a fast algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x.
Installing R packages on Atmosphere Jun 23, 2016 Install R packages on Atmosphere: Launch instance, transfer files to instance, install R package, request imaging.
QIIME-1.9.1 for Atmosphere Jun 12, 2017 QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA
rnaQUAST 1.2.0 May 19, 2016 rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene data database. In addition, rnaQUAST is also capable of estimating gene database coverage by raw reads and de novo quality assessment using third-party software (STAR, TopHat, GMAP etc.).
QUAST 4.0 May 19, 2016 QUAST is a tool for evaluating genome assemblies by computing various metrics.
rnaQUAST 1.1.0 May 11, 2016 rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene data database. In addition, rnaQUAST is also capable of estimating gene database coverage by raw reads and de novo quality assessment using third-party software (STAR, TopHat, GMAP etc.).
Evolinc May 03, 2016 Evolinc is a two-part pipeline to identify lincRNAs from an assembled transcriptome file (.gtf output from cufflinks) and then determine the extent to which those lincRNAs are conserved in the genome and transcriptome of other species.
FaST-LMM.Py v2.02 Apr 19, 2016 Introduce new users to the FaST-LMM software for GWAS analysis.
KOBAS 2.0-09052014 Apr 19, 2016 Learn how to annotate and identify using KOBAS 2.0.
Validate Workflow v0.9 Apr 19, 2016 Learn to navigate the Validate Workflow.
BATools 0.0.1 Apr 10, 2016 Introduce new users to BATools and the BATools Wrapper Script.

Geoinformatics Tutorials Using CyVerse

Tutorial Date Notes
NEON AOP Workshop Nov 11, 2021 Second virtual NEON AOP Workshop in collaboration with USDA-ARS and UArizona RISE Conference
NEON AOP Workshop Nov 05-07, 2020 First virtual NEON AOP Workshop in collaboration with USDA-ARS and UArizona RISE Conference
NEON-CyVerse Workshop Jan 09, 2019 CyVerse Workshop taught at Battelle Inc. NEON Headquarters, Boulder CO
NEON Data Science Institute July 12, 2018 NEON summer workshop taught at Battelle Inc. NEON Headquarters, Boulder CO

Astronomy Tutorials Using CyVerse

Workshop Date Description
Cloud Computing Busy Week Feb 2-7, 2020 a five-day busy week was conducted at the University of Arizona in order for PIRE members to work on large-scale synthetic data generation for the Event Horizon Telescope (EHT) project
AstroContainers Workshop May 7-8, 2018 designed for astronomers and astrophysicists at Steward, LSST, NOAO, and LPL
MiniHackathon PIRE Apr 11, 2018 Docker and Jupyter for Reproducible Astronomy

Last update: 2022-09-28