# Next-Gen Sequence Analysis Workshop (2018) These are the schedule and classroom materials for the [ANGUS workshop at UC Davis](http://ivory.idyll.org/dibsi/ANGUS.html), which will run from July 2nd to July 14th, 2018. ANGUS is part of the 2018 [Data Intensive Biology Summer Institute](http://ivory.idyll.org/dibsi/). This workshop runs under a [Code of Conduct](code-of-conduct.html). Please respect it and be excellent to each other! Twitter hash tag: [#dibsi2018](https://twitter.com/search?f=tweets&q=%23dibsi2018&src=typd) ## Rooms and lead instructors! There are three rooms - Lions, Tigers and Bears! Lions will be ably led by Dr. Elijah Lowe and Adam Orr, in 1041 Valley. Tigers will enjoy the leadership of Dr. Amanda Charbonneau and Dr. Fotis Psomopoulos, in 1043 Valley. Dr. Tristan De Buysscher and Lisa Johnson will lead Da Bears through the forest, in 1047 Valley. ## Schedule, in brief: Monday 7/2: * 1:30-5:30pm - welcome & getting started with Jetstream - 1030 Valley Hall. * [Welcome slides](https://docs.google.com/presentation/d/1bAfTYNigeYXC1EWrjpAEaFc9zWd_JxXlk9DJ99MXo7g/edit#slide=id.g3cc5aa73e1_0_81) * [Booting from Jetstream](https://angus.readthedocs.io/en/2018/jetstream/boot.html) * [Intro to collaboration tools](https://angus.readthedocs.io/en/2018/online-tools.html) * [Running BLAST at the command line](https://angus.readthedocs.io/en/2018/running-command-line-blast.html) * [Visualizing BLAST scores](https://angus.readthedocs.io/en/2018/visualizing-blast-scores-with-RStudio.html) Tuesday: * morning speaker: Titus [(slides)](https://osf.io/cp8tw/) * 9am-noon - lab/lecture/instruction * [Quality trimming etc](https://angus.readthedocs.io/en/2018/quality-and-trimming.html) * noon-1:15 - lunch break (lunch on your own) * 1:15-5:30pm - tutorials * continued from above. Wednesday 7/4: * 9am-noon - tutorials * [Mapping and variant calling](https://angus.readthedocs.io/en/2018/mapping-variant-calling.html) * BREAK for the day - July 4th activites Thursday: * 9am-noon - tutorials * [Mapping and variant calling, cont'd](https://angus.readthedocs.io/en/2018/mapping-variant-calling.html) * noon-1:15 - lunch (lunch on your own) * 1:15-5:30pm - tutorials * [RNAseq and differential expression](https://angus.readthedocs.io/en/2018/rna-seq.html) Friday: * 9am: morning lecture: Amanda, on statistics and experimental design [(slides)](https://github.com/ngs-docs/angus/blob/2018/StatsNstuff.pdf) * 10:15-noon - tutorials * [RNAseq and differential expression, cont'd](https://angus.readthedocs.io/en/2018/rna-seq.html) * noon-1:15 - lunch (lunch on your own) * 1:15-5:30pm - tutorials * [Transcriptome assembly](https://angus.readthedocs.io/en/2018/transcriptome-assembly.html) * Challenge exercise: [assemble this genome!](genome-assembly.html) ## Second week, July 9-July 14. Monday * 9-10am: week2 orientation, Titus Brown * 10:15am-noon: * Lions: An -omics chat * Tigers: [Configuring your Jetstream computer](jetstream-bioconda-config.html) * Bears: [Configuring your Jetstream computer](jetstream-bioconda-config.html) * * noon-1:15 - lunch (lunch on your own) * 1:15-3pm: * Lions: [Configuring your Jetstream computer](jetstream-bioconda-config.html) * Tigers: An -omics chat * Bears: [RMarkdown](rmarkdown_rnaseq.html) * 3:15pm-5:15pm: * Lions: [RMarkdown](rmarkdown_rnaseq.html) * Tigers: [RMarkdown](rmarkdown_rnaseq.html) * Bears: An -omics chat Tuesday: * 9-10am: morning speaker: Erich Schwarz [(slides)](https://osf.io/hwnby) * 10:15am-noon - [ChIP-seq and UCSC pileup](chip-seq.html) * noon-1:15 - lunch break (lunch on your own) * 1:15:3pm - [transcriptome annotation](dammit_annotation.html) * 3:15pm-5:30pm - topic specific breakouts * Microbial ecology & microbiome (Mike & Sabah) [(notes)](https://hackmd.io/bXyY0ttZSGaIFcnvwdKEVw?view) * Non-model -omics (Elijah and Lisa) * Model organisms (Erich, Rocio) [(notes)](https://hackmd.io/Xca7-YOVQ9iwvpuW2zBp5g) * Population genetics / comparative genomics / GWAS (Shannon, Kat, Elias) * Work on your own (Adam) * 5:30pm-7:30pm - dinner (on your own) * 7:30-9pm: posters & ice cream session Wednesday: * 9-10am: morning speaker: Torsten Seemann [(slides)](_static/BacterialGenomics_TorstenSeemann_DIBSI_2018-07-11.pdf) * 10:15am-noon: [transcriptome annotation](dammit_annotation.html), cont'd. * noon-1:15 - lunch (lunch on your own) * 1:15-4pm: * lions: [transcriptome annotation](dammit_annotation.html), cont'd. * tigers: automation by snakemake pilot, by Titus (will start at 1:35pm #childcare) * bears: [where to put your data pilot](where_to_put_data.html) * 4pm - end of day (farmer's market downtown) Thursday: * 9-10am: morning speaker: Sam Diaz-Munoz * 10:30am-12:15pm: * lions: assembly tutorial (Torsten) * tigers: [where to put your data](where_to_put_data.html) * bears: [snakemake tutorial](https://hackmd.io/s/Bkatoy47X) (Sateesh) * 12:30pm-1:30 - lunch (lunch on your own) * 1:30-3:15pm: * lions: [where to put your data](where_to_put_data.html) * tigers: work on your own interests * bears: work on your own interests * 3:15-3:45pm: Tea Time! Photos! * 3:45pm-5:30pm - lab/lecture/instruction * lions: [automation via snakemake tutorial](https://hackmd.io/s/B1aL7_lmQ#) (Titus) * tigers: assembly tutorial (Torsten) * bears: Next steps working group Friday: * 9-10am: morning speaker: Luis Carvajal (slides will not be posted) * 10:30am-12:15pm: * lions: sourmash tutorial (Phillip Brooks) * [K-mers, k-mer specificity, and comparing samples with k-mer Jaccard distance](https://angus.readthedocs.io/en/2018/sourmash.html) * tigers: Next steps working group. * bears: Torsten tutorial * 12:30pm-1:30 - lunch (lunch on your own) * 1:30-3:15pm: breakout tutorials!! locations TBD. * Amplicon & microbial ecology (Mike and Sabah) * come to do your choice of a number of [amplicon tutorials](https://hackmd.io/1z4q6wtcRLGQzVUhfaphbA?view#Testing-it-out-with-a-practice-dataset) or a [metagenomics tutorial of recovering genomes from metagenomes](https://angus.readthedocs.io/en/2018/metagenomics_anvio.html)! - work with practice data or your own data! - we will be there for individual/group help/discussion, installing tools trouble, etc. :) * Some more R, Shiny, and the tidyverse (Amanda and Rocio) * More UNIX shell (Fotis) * Comparative microbial genomics (Torsten) * 3:15-3:45pm: Tea Time! * 3:45-5:30pm - lab/lecture/instruction * lions: Next steps working group * tigers: [sourmash tutorial](sourmash.html) (Phillip Brooks) * bears: [sourmash tutorial](sourmash.html) (Titus) Saturday - (check out of your rooms and bring luggage over) **Please bring your computer on Saturday.** * 9am: [What does the future hold in a world of infinite data?](https://osf.io/fajd5/) (Titus) * 10:15am: * "one up/one down" assessment (in each room) * DIBSI '19 organizational meeting (helpers & instructors) - 1030 * 11am: * report back * thanks and fare-thee-well!