Shaun Jackman

@sjackman

I develop Cell Ranger at 10x Genomics, Homebrew, and developed ABySS for my PhD at UBC. I cook, sing, travel, see theatre, and play boardgames for fun. 🏳️‍🌈

Vancouver, Canada

sjackman.ca

Joined September 2007

Pinned
Shaun Jackman
@sjackman
Nov 27, 2019
🧬 10x Genomics is hiring! My first three months at 10x have been fantastic. My colleagues are friendly and helpful. 10x is based in Pleasanton, CA. Remote work may be possible, depending on the position. Check out open positions at grnh.se/c3f537b11
Shaun Jackman
@sjackman
Jun 21, 2022
Is there a tool to index a BGZIP-compressed FASTQ file and extract a range of reads, like the 1,000,000–2,000,000th reads? There's grabix, and hacks converting FASTQ to TSV and using tabix, or putting the record number in the position column of SAM and using samtools index/view.
Shaun Jackman
@sjackman
Feb 17, 2022
Who's serving whom here?
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Shaun Jackman
@sjackman
Jan 25, 2022
*For *odd* values of k…
Shaun Jackman
@sjackman
Jan 24, 2022
Replying to @pashadag
github.com/bcgsc/abyss/bl… For even values of k, ABySS splits unitigs at palindromic (k-1)-mers to prevent both a k-mer and its reverse complement from appearing in the unitig.
Shaun Jackman
@sjackman
Jan 24, 2022
> ABySS clearly exhibits the palindrome splitting artifact, with all non- ambiguous unitigs being split and none fully-covered. It's by design and intentional that ABySS splits palindromic unitigs. ABySS ensures that each k-mer and its RC is present at most once in the unitigs.
PM @[email protected] @pashadag.bsky.social
@pashadag
Jan 24, 2022
In a new paper with @amatur_r, we investigated how de Bruijn graph-based assemblers exhibit systematic mis- and under-assemblies that is inherent to unitigs. x.com/biorxiv_bioinf… 1/6