Erin Young
@erinyoung.bsky.social
Public Health #Bioinformatician. Wants to sequence ALL THE THINGS. Personal account with alternative spellings and grammar structures. She/her
This is my first time working with NeighborNet (part of phangorn), and I think I'm going to need to do some reading so that 1) this makes sense to me, and 2) I can explain it to my collaborators
October 28, 2025 at 10:34 PM
This is my first time working with NeighborNet (part of phangorn), and I think I'm going to need to do some reading so that 1) this makes sense to me, and 2) I can explain it to my collaborators
I had an EPI contact me to see if any isolates were clustering with 2024CK-00004 and 2024CK-00250 for EPI reasons. Pathogen Detection has these two isolates in the same cluster, making this question relatively easy to answer.
October 17, 2025 at 5:35 PM
I had an EPI contact me to see if any isolates were clustering with 2024CK-00004 and 2024CK-00250 for EPI reasons. Pathogen Detection has these two isolates in the same cluster, making this question relatively easy to answer.
I probably need some different colors, but I've made a graph detailing the number of AMR genes we've seen in organisms that we've sequenced for the last few months.
October 16, 2025 at 6:10 PM
I probably need some different colors, but I've made a graph detailing the number of AMR genes we've seen in organisms that we've sequenced for the last few months.
And today's (useless) figure is that the mean depth observed in a bam file is linearly associated with the number of reads in the corresponding fastq files.
September 29, 2025 at 5:04 PM
And today's (useless) figure is that the mean depth observed in a bam file is linearly associated with the number of reads in the corresponding fastq files.
I think you misunderstand. There is a lot of coverage for these samples. So much so that it is hard to see bubbles or other aberrations.
September 23, 2025 at 8:46 PM
I think you misunderstand. There is a lot of coverage for these samples. So much so that it is hard to see bubbles or other aberrations.
Mine does this too! The library reminds me that my kids would bankrupt me if I didn't have a library nearby.
August 12, 2025 at 4:08 PM
Mine does this too! The library reminds me that my kids would bankrupt me if I didn't have a library nearby.
Which gives me images like these. So far, these primers seems to be functional. /
August 8, 2025 at 9:03 PM
Which gives me images like these. So far, these primers seems to be functional. /
This primer scheme is different than the other schemes I've worked with because there are so many overlapping regions. For example, positions 412-433 of NC_001498.1 could be amplified by any of seven different primer pairs. /
August 8, 2025 at 9:03 PM
This primer scheme is different than the other schemes I've worked with because there are so many overlapping regions. For example, positions 412-433 of NC_001498.1 could be amplified by any of seven different primer pairs. /
I didn't mean to fail the internet!
August 8, 2025 at 8:43 PM
I didn't mean to fail the internet!
Currently having an intern test how normalization impacts coverage for amplicon libraries. This one is normalized to 500X coverage.
August 7, 2025 at 5:16 PM
Currently having an intern test how normalization impacts coverage for amplicon libraries. This one is normalized to 500X coverage.
I thought this facility had gotten their #CRPA under control, but two new patients appear to cluster with the ones from 2022 and 2023.
(Also, I work with some great epis who are on top of this in order to keep our healthcare facilities safe)
🧬🖥️🦠
(Also, I work with some great epis who are on top of this in order to keep our healthcare facilities safe)
🧬🖥️🦠
May 13, 2025 at 4:26 PM
I thought this facility had gotten their #CRPA under control, but two new patients appear to cluster with the ones from 2022 and 2023.
(Also, I work with some great epis who are on top of this in order to keep our healthcare facilities safe)
🧬🖥️🦠
(Also, I work with some great epis who are on top of this in order to keep our healthcare facilities safe)
🧬🖥️🦠
Not to ruin the punchline, but the images of this preprint are top tier.
April 9, 2025 at 7:23 PM
Not to ruin the punchline, but the images of this preprint are top tier.
It's the end of an era. I wish they hadn't died on me.
March 28, 2025 at 8:15 PM
It's the end of an era. I wish they hadn't died on me.
Sometimes, nanopore-only assemblies are just easier to use.
March 7, 2025 at 5:11 PM
Sometimes, nanopore-only assemblies are just easier to use.
One of *my* clusters on pathogen detection is PDS000214655, meaning almost every sequence was from submissions I've been involved in. Samples are from 2023-2025. 🧬🖥️🦠
February 28, 2025 at 5:12 PM
One of *my* clusters on pathogen detection is PDS000214655, meaning almost every sequence was from submissions I've been involved in. Samples are from 2023-2025. 🧬🖥️🦠
One my yearly highlights is meeting with young minds as a judge for a local STEM fair (previously called science fairs).
The future is bright my friends!
The future is bright my friends!
February 25, 2025 at 6:22 PM
One my yearly highlights is meeting with young minds as a judge for a local STEM fair (previously called science fairs).
The future is bright my friends!
The future is bright my friends!
I've become a long-read snob. We sequenced this isolate (534,166 #ont reads with an average length of 2,611.5 bp), and I want to sequence the isolate again because I think we can resolve the plasmids better.
February 14, 2025 at 5:57 PM
I've become a long-read snob. We sequenced this isolate (534,166 #ont reads with an average length of 2,611.5 bp), and I want to sequence the isolate again because I think we can resolve the plasmids better.
We are soooo close to having COVID results in our LIMS system
![A drop down menu with some green tube-ish icons.
NGS_COV_SEQ [COVID Whole-genome Sequencing]
- Run Name
- Submission Accession
- Non Ambiguous Bases
- Passed QC
- Nextclade Clade
- Lineage](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:iegfpv4ewkby2fk6u5iea34c/bafkreifknjkwaj3grs2fdyrtjl4cywe2mlb4d5o2to7qtusr6237z74q6m@jpeg)
February 11, 2025 at 5:05 PM
We are soooo close to having COVID results in our LIMS system
My new guidebook on science communication
November 6, 2024 at 9:50 PM
My new guidebook on science communication
PERFECT!!! I actually have two items that I am stuck on:
1. Do you happen to have coordinates or a fasta file for "The Francisella pathogenicity island"
2. Do you happen to have to start and end coordinates for this figure? (Figure 1 from pmc.ncbi.nlm.nih.gov/articles/PMC...)
1. Do you happen to have coordinates or a fasta file for "The Francisella pathogenicity island"
2. Do you happen to have to start and end coordinates for this figure? (Figure 1 from pmc.ncbi.nlm.nih.gov/articles/PMC...)
October 22, 2024 at 10:56 PM
PERFECT!!! I actually have two items that I am stuck on:
1. Do you happen to have coordinates or a fasta file for "The Francisella pathogenicity island"
2. Do you happen to have to start and end coordinates for this figure? (Figure 1 from pmc.ncbi.nlm.nih.gov/articles/PMC...)
1. Do you happen to have coordinates or a fasta file for "The Francisella pathogenicity island"
2. Do you happen to have to start and end coordinates for this figure? (Figure 1 from pmc.ncbi.nlm.nih.gov/articles/PMC...)