Mao-Jan Lin

PhD Student @JHUCompSci

[Mao-Jan Lin @MaoJanLin]

gAIRR-Suite is a new toolkit profiling genes encoding the Adaptive Immune Receptor Repertoire (AIRR). We combined experimental and computational methods to genotype both documented and novel V, D, J genes in the human germline genome. 1/
https://t.co/IpqRSabiRA

[Mao-Jan Lin @MaoJanLin]

7/ Huge thanks to my advisor @BenLangmead for the guidance and support, and my collaborator @vikshiv1 !

Code is available from https://t.co/QrZTeujPR0

[Mao-Jan Lin @MaoJanLin]

1/ Excited to share our preprint ImpuT2T: a pangenome-based assembly patching tool!

ImpuT2T scaffolds draft human assemblies with a pangenome (HPRC2) and patches gaps via sequence identity between contigs and reference haplotypes.

https://t.co/sQHcOhVkfF

[Mao-Jan Lin @MaoJanLin]

6/ Although runtime scales linearly with the number of haplotypes, ImpuT2T is highly parallelizable:
- Runs in ~15 hours (48 threads) on the full 470-haplotype pangenome.
- If your compute node can handle de novo assembly, it can run ImpuT2T with HPRC2.

[Kuan-Hao Chao @KuanHaoChao]

Excited to announce Splam is now published in @GenomeBiology! Splam, trained on thousands of splice junctions from GTEx, is your go-to tool for scoring splice junctions from alignment or annotation files.
@elapertea @StevenSalzberg1 @alan_mayonnaise

https://t.co/52pYjGhuRk

[Javier Santoyo @jsantoyo]

Measuring, visualizing, and diagnosing reference bias with biastools. #AnalysisBias #GenomicsData #Bioinformatics @BenLangmead @GenomeBiology
https://t.co/U5bKPqUc4O

[Alex Sweeten @alexsweeten]

Happy to share our preprint for ModDotPlot - Rapid and Interactive Visualization of Complex Repeats https://t.co/AalUjZblvp

[Kuan-Hao Chao @KuanHaoChao]

📢📢Dear friends, I'm thrilled to introduce LiftOn, our new homology-based annotation lift-over tool🚀 Join my talk at @RECOMBseq Saturday April 27th at 2:50PM!
@JakobHeinz9 @celinehohzm @alan_mayonnaise @alaina_shumate @elapertea @StevenSalzberg1
🔗https://t.co/1IQjtk5LkD (1/5)

[Corey Watson @ctwatson29]

On AIRR 15: Germline databases or adventures into the allelic underworld with Dr. Corey Watson and Dr. William Lees https://t.co/J9yuXTHBgU

[Corey Watson @ctwatson29]

Stellar work by @e_engelbrecht1 (@olrodriguez_ ; @SmithLab_UofL) -- Resolving haplotype variation and complex genetic architecture in the human immunoglobulin kappa chain locus in individuals of diverse ancestry https://t.co/TxALus507y

[Mao-Jan Lin @MaoJanLin]

Many thanks to @BenLangmead and @naechyun_chen for advising of this work! end/

[Mao-Jan Lin @MaoJanLin]

Recent alignment methods aim to reduce reference bias, where reads with non-ref alleles fail to align correctly. However, there's a lack of methods for analyzing reference bias. Here we present biastools, which measures and categorizes reference bias. 1/
https://t.co/Xcp1AoKkob

[Mao-Jan Lin @MaoJanLin]

Easy installation through pip. Feedbacks are welcome! 8/
https://t.co/0BVJQIqQCn