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Next-Gen Sequence Analysis Workshop (2016) — angus 5.0 documentation

Angus 5.0 documentation. Next-Gen Sequence Analysis Workshop (2016). This is the schedule for the 2016 MSU NGS course. All course communications will be organized around the Slack channel. This workshop has a. Workshop Code of Conduct. Download all of these materials. Or visit the GitHub repository. Meal Times: Breakfast 7:45-8:45, Lunch 12-1, Dinner 6-7 (Unless noted below). See HERE. For the menu and other info. 2:30pm: Getting Started with AWS. Getting started with Amazon EC2. 4pm: Intro to Linux.

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Next-Gen Sequence Analysis Workshop (2016) — angus 5.0 documentation | angus.readthedocs.io Reviews

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Angus 5.0 documentation. Next-Gen Sequence Analysis Workshop (2016). This is the schedule for the 2016 MSU NGS course. All course communications will be organized around the Slack channel. This workshop has a. Workshop Code of Conduct. Download all of these materials. Or visit the GitHub repository. Meal Times: Breakfast 7:45-8:45, Lunch 12-1, Dinner 6-7 (Unless noted below). See HERE. For the menu and other info. 2:30pm: Getting Started with AWS. Getting started with Amazon EC2. 4pm: Intro to Linux.

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Next-Gen Sequence Analysis Workshop (2016) — angus 5.0 documentation | angus.readthedocs.io Reviews

https://angus.readthedocs.io

Angus 5.0 documentation. Next-Gen Sequence Analysis Workshop (2016). This is the schedule for the 2016 MSU NGS course. All course communications will be organized around the Slack channel. This workshop has a. Workshop Code of Conduct. Download all of these materials. Or visit the GitHub repository. Meal Times: Breakfast 7:45-8:45, Lunch 12-1, Dinner 6-7 (Unless noted below). See HERE. For the menu and other info. 2:30pm: Getting Started with AWS. Getting started with Amazon EC2. 4pm: Intro to Linux.

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angus.readthedocs.io

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Assembly Quest — angus 5.0 documentation

http://angus.readthedocs.io/en/2016/MacManes_AssemblyQuest.html

Angus 5.0 documentation. I am going to give you some data and a genome (well, 500Mb of the genome). Please assemble and use BUSCO. Launch an AMI. For this exercise, try a c4.8xlarge. With a 200Gb EBS volume. Wow yes this is a BIG machine! You will need to install. Installing BUSCO is a bit of a PITA. Here is the way, once you have brew installed. They have already been trimmed for you :). Use ABySS to assemble reads. You have 32 threads to use! I suggest you use them all. You’ll need to download an...

2

Map Quest — angus 5.0 documentation

http://angus.readthedocs.io/en/2016/MacManes_MapQuest.html

Angus 5.0 documentation. I am going to give you some data and a genome (well, 500Mb of the genome), I want you to quality trim and map using the Trimming lecture and the Mapping Lecture. Launch an AMI. For this exercise, try a c4.4xlarge. With a 200Gb EBS volume. You will need to install. Download the genome and the reads. Use Skewer to trim reads. For people whose 1st name starts with between A-F, skip this step to allow us to evaluate the performance of mapping untrimmed reads. Map the reads with BWA.

3

Variant calling — angus 5.0 documentation

http://angus.readthedocs.io/en/2016/variant.html

Angus 5.0 documentation. The goal of this tutorial is to show you the basics of variant calling using Samtools. We’re going to be looking at variation in laboratory grown strains of Escherichia coli. We have reads from B strain REL606 and we’ll be mapping it to a reference genome from BL21(DE3). This is a different lab strain, and there’s an interesting paper where they trace the origin and transfer of all the different E. coli strains between scientisits through the decades. Booting an Amazon AMI. Curl ...

4

UNIX Toolkit — angus 5.0 documentation

http://angus.readthedocs.io/en/2016/MacManes_UNIX.html

Angus 5.0 documentation. The explicit goal of this tutorial is to provide you with some tricks and tools and to make your unix life happier. See https:/ github.com/stephenturner/oneliners. For a bunch of examples. Profile customization and aliases. These are ‘shortcuts’ for make doing stuff more efficient. Raw=true quantification.tgz tar -zxf *gz. Cd $HOME find / -name quant.sf find / -type f -size 10M 2 /dev/null. A helpful guide to sed. Number fasta def line. Presentations (PPT/PDF) and PDFs are the pr...

5

Population Genetics Tutorial — angus 5.0 documentation

http://angus.readthedocs.io/en/2016/pop_gen_tutorial.html

Angus 5.0 documentation. Before you guys got here. Started with data from: “Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake”, Malinsky et al 2015. Downloaded VCF from http:/ datadryad.org/resource/doi:10.5061/dryad.770mc. Http:/ datadryad.org/bitstream/handle/10255/dryad.101389/Massoko Dryad VCF final.vcf.gz. These data had been filtered for quality. And only variable sites had been retained. And phased using the program. Start your instance with at least 50 Gb&#46...

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Adventures with ONT MinION at MBL’s Microbial Diversity Course | Lisa Johnson Cohen

https://monsterbashseq.wordpress.com/2016/08/13/adventures-with-ont-minion-at-mbls-microbial-diversity-course

Notes on PhD research learning R, Python and Linux for bioinformatics and genomic-scale data analyses. Computing Workflows for Biologists – Dr. Tracy Teal. MMETSP re-assemblies →. Adventures with ONT MinION at MBL’s Microbial Diversity Course. August 13, 2016. My time here at the Microbial Diversity Course. Has come to an end after visiting for the past 2 weeks with our lab’s. Sp isolated by Rebecca Mickol). In Titus Brown’s DIB lab. Assemblies from existing Illumina data. For MinION users, but a login i...

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Next-Gen Sequence Analysis Workshop (2016) — angus 5.0 documentation

Angus 5.0 documentation. Next-Gen Sequence Analysis Workshop (2016). This is the schedule for the 2016 MSU NGS course. All course communications will be organized around the Slack channel. This workshop has a. Workshop Code of Conduct. Download all of these materials. Or visit the GitHub repository. Meal Times: Breakfast 7:45-8:45, Lunch 12-1, Dinner 6-7 (Unless noted below). See HERE. For the menu and other info. 2:30pm: Getting Started with AWS. Getting started with Amazon EC2. 4pm: Intro to Linux.

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