Comparing Short Read Polishers

Posted on Fri 06 September 2019 in genomics • Tagged with genome assembly, genomics, plantsLeave a comment

"Polishing" is the process of using short accurate Illumina sequencing reads to correct errors in noisy draft genome assemblies. Here, I will try out a few popular short-read genome assembly polishing tools/techniques and compare their efficacy by looking at assembly k-mer content. We will start with a draft genome assembly of a modern cultivated tomato line. This line was sequenced with ONT Continue reading


Reference-Guided Assembly Scaffolding With RaGOO

Posted on Thu 31 January 2019 in genomics • Tagged with genome assembly, genomics, plantsLeave a comment

Nowadays, assembling large eukaryotic genomes is more accessible than ever. This is in large part due to the fact that Oxford Nanopore Technologies (ONT) has made tremendous strides towards improving the throughput of their sequencers.

For example, Michael et al. recently described the ability to obtain highly-contiguous Arabidopsis thaliana assemblies from a single MinION flow-cell. It's also becoming clear that the PromethION is reaching insanely high levels of throughput, producing Terabases of data in just days.

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Assembly-Based Inversion Calling

Posted on Tue 11 September 2018 in genomics • Tagged with genomics, structural variantsLeave a comment

Both WGS alignment methods and whole genome alignment methods are used to computationally identify structural variants (SVs). Assemblytics is an example of a whole genome alignment method, as it scans nucmer alignments of a query genome to a reference genome to call variants. However, Assemblytics only calls insertions and deletions (and expansions and contractions, but we can consider those insertions and deletions respectively). In an effort to expand this software, I want to add the ability to call more types of variants such as inversions and translocations. Here, I focus on inversions and begin to investigate how very simple inversions appear in genome-genome alignments.

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Sugarcane Genomics Review

Posted on Mon 29 January 2018 in genomics • Tagged with plants, genomicsLeave a comment

I have recently started working on a sugarcane genome assembly project, so I figured I would share some interesting points from my literature review. Sugarcane is obviously a very economically important crop, having applications in both food and energy production. Despite this economic importance, genomic resources are lacking for sugarcane due to the complexity of the genomes of modern cultivars. Let's look into the specifics of why that is.

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Random Music With Python

Posted on Fri 12 August 2016 in python • Tagged with python, musicLeave a comment

At PyCon 2016 I attended a very interesting session entitled Learning Python Through Music: JythonMusic & Pyknon, presented by Ria Baldevia. The talk was a great introduction to some python APIs that allow for the creation of music using the python language. Here I will demonstrate how to use the pyknon library, and some of the fun things one can do taking a programmatic approach to creating music.

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