yq

A bioinformatician beginner. Interested in NGS and long-reads sequencing.

[BioDecoded @BioDecoded]

A survey of algorithms for the detection of genomic structural variants from long-read sequencing data | Nature Methods
https://t.co/su2dX9kcTj

#Bioinformatics

[yq @conanyangqun]

@ninadoak using singularity instead of docker for many users environment，such as hpc

[Kishwar @kishwarshafin]

Very important work shown here.

Excited about R10 and the improvements we will see this year. Happy to be a part of this work.

[yq @conanyangqun]

@CloudGenomics what about wdl and snakemake？

[Simona Cristea @simocristea]

Can't keep up with all the interesting #ChatGPT prompts?

Nothing to worry about! I curated a 🧵for you with key messages & relevant tweets on where our new academic companion #ChatGPT excels or fails in writing #Bioinformatics code, academic grants & tutorials👇

[yq @conanyangqun]

@KoenDeserranno @TJesse62 @nanopore @illumina @nxtgnt 👏👍

[Andrew Beggs @adbeggs]

Another @nanopore sequencing blinder from @JoStockton1 in @beggs_lab:
Apparently you can't amplify methylated DNA and maintain the methylation - well you can!
Top sample - conventional WGA
Middle sample - methWGA
Bottom sample - original sample

[MIT CSAIL @MIT_CSAIL]

9 key computer science topics - and the best book and video for learning each of them: https://t.co/i6qNiE8qhr (credit @BradfieldCS)

[yq @conanyangqun]

@KoenDeserranno @TJesse62 @nanopore @illumina @nxtgnt how much total data do you get？the whole flowcell，thx

[Koen Deserranno @KoenDeserranno]

@TJesse62 @nanopore @illumina @nxtgnt Indeed, using AS on PromethION on a first DNA sample, targeting 0.7% of the human genome. Median on-target coverage about 90X, about 6 times enrichment vs regions outside .bed file. Run still done using LSK110 on R.9.4.1 flow cell, next month using LSK114 on R 10.4.1 !

[Broad Institute @broadinstitute]

.@BlaineyLab teams up with @WhiteheadInst's @iaincheeseman to explore the function of >5,000 essential human genes using a massive, #CRISPR-based, pooled optical screening approach. #functionalgenomics https://t.co/Fz1fj1m9FS

[Adam Phillippy @aphillippy]

The #T2T team is excited to release our first draft of a complete, diploid human genome for the @GenomeInABottle benchmark sample, HG002! Links to the data and assembly can be found here: https://t.co/tYb4oamaVS 🧵

[Oxford Nanopore @nanopore]

Register for NCM 2022! Oxford Nanopore heads to New York this December to showcase some of the best #nanopore sequencing research. #nanoporeconf

Register here for online or in-person: https://t.co/kMqTQx0kgO

[Hasindu Gamaarachchi @Hasindu2008]

Introducing squigulator, a tool for simulating nanopore raw signal data:
https://t.co/ikhQOPszxI
After simulating signals you can basecall, map and variant call if you wish.

In development stage, so feature requests, feedback (+ or -) and comments are welcome.

[Oxford Nanopore @nanopore]

With PromethION 24, combine long sequencing reads (up to 4 Mb) with high sample throughput to generate highly contiguous human genomes, with resolution & phasing of SNVs, SVs, repeats, & DNA methylation in a single assay. Check out the resources below to learn more. 1/5

[Eric Green @NHGRI_Director]

Whether you want to bring genomics into your classroom or are just curious about genomics, @genome_gov can help. I may be biased, but we cover lots of fascinating genomics topics in our fact sheets! https://t.co/kgAJj9NR3K

[Robert Aboukhalil @RobAboukhalil]

Here are some interesting datasets to explore:

- Telomere-to-telomere human genome by @HumanPangenome: https://t.co/eyyTubIgrV
- COVID-19 data by @DNAstack: https://t.co/GjGIN8a0uW
- Benchmarking data by @GenomeInABottle: https://t.co/9MmBgLXzzI

More: https://t.co/CLVcNZzCpJ

[Oxford Nanopore @nanopore]

'Excitingly, LSK114 kit with flow cell R10.4.1 released in London Calling 2022 not only maintains the accuracy of 99%, but also improves the sequencing yield to the same level or even more as LSK109 kit with flow cell R9.4.1': https://t.co/N0awW9gCLH

[Stéphane Le Crom @slecrom]

Adaptive Sampling as tool for Nanopore direct RNA-sequencing https://t.co/xrI2IJikSA