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DLBPointon/README.md

Hi, I'm Damon


👨‍💻 About Me:

I'm a Bioinformatian working at Sanger Wellcome Genome Campus (UK) inside ToLA (Tree of Life Assembly Team). My day-to-day role includes building Nextflow Pipelines, namely TreeVal, for the scaling of genomic analysis.

🔥 My Stats :

My GitHub contributions may appear as either DLBPointon or as dp24.

GitHub Streak

Top Langs

During my time at these institutes I have gained a significant amount of experience in:

HTML and Javascript

  • In creating a number of full stack projects, such as GRIT-realtime (for use at Sanger where it integrates with the local JIRA platform), university projects such as a COVID tracker which is still viewable Here as portfolio evidence.

  • In personal projects. I use a tool called Obsidian a second brain designed to powerful and customisable whilst making use of Markdown. In light of this I have written QuickAdd-NCBI, which adds taxonomic data from NCBI into a note, and contributed to a number of projects which extend the use of Obsidian such as QuickAdd-Books, Booksidian and Obsidian-Plotly. In the future I plan to create a full plugin to integrate a wider breadth of the NCBI API into Obsidian, especially due to the large number of biologists and bioinformaticians that use the software.

  • Javascript. Due to experience from the above I have al written a significant amount of JS as well as some small Javascript scripts for ToLQC which graph various statistics.

Python

  • I have used Python in almost every project I have been involved with during my time at ARU and Sanger. The first being gEVAL_cleaner, this script would download cdna, cds, rna and protein data of a given organism and prepare it for use in genomic alignment.

  • Some components of GRIT-realtime were also written in Python, namely the script which pulls data from JIRA and massaged it into the format required for database uploading

  • I have also written a number of "bots", simple reporting scripts most of which pull various data from JIRA and post them to Slack channels. BTK-announcer relays ticket information on BlobTookKit requests to those involved with decontamination, Priority-list relays information on high priotity tickets to all, Weekly-report reports on what tickets have changed hands over the course of the past week for management.

  • There are also a number of smaller scripts, I haven't uploaded to GitHub. These include projects in gene expression over time, simple graphing and data parsing.

Pipelines

  • Snakemake. For a universioty project, I wrote a variant annotation pipeline using Illumina data.

  • Nextflow DSL2. I am currently working on translating the Snakemake annotation pipeline into Nextflow for wider adoption at Sanger in the DTOL project, This will be using the nf-core production guidelines, allowing for "plug and play" functionality.

  • I have also aided in the building of TeloSearch and TreeVal (NF-core standard), both of which are DSL2 pipelines in use at Sanger.

  • 🌱 I am also currently learning; Rust in order to modernise some software in use at Sanger, Angular and it's integration with PostgREST/PostgreSQL for a personal project and delving deeper into JavaScript to build plugins for the Obsidian Community.

Pinned Loading

  1. covid19-graphs-DLBPointon covid19-graphs-DLBPointon Public

    covid19-graphs-DLBPointon

    Jupyter Notebook

  2. grit-weeklyreport grit-weeklyreport Public

    Simple JIRA reporting script for use in GRIT

    Python

  3. annotation-pipeline-snakemake annotation-pipeline-snakemake Public

    An annotation pipeline written for ARU/Sanger assessments.

    Python

  4. sanger-tol/variantcalling sanger-tol/variantcalling Public

    This Nextflow DSL2 pipeline calls variants on long read alignment. It is run after sanger-tol/readmapping in the Sanger ToL production suite but with options to run on unaligned reads.

    Nextflow 3 2

  5. AlanTracey99/TeloSearch AlanTracey99/TeloSearch Public

    Python