Wei Shen 沈 伟
@shenwei356
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Associate professor of Bioinformatics at Chongqing Medical University, China. Developing tools for microbial (meta)genomics. BlueSky: https://t.co/mXnnqslpi1
Chongqing, China
Joined November 2013
Excited to share this collaborative work with @ZaminIqbal ! We're thrilled about the potential impact LexicMap could have on advancing microbial genomics research! Imagine how cool it is to search for a gene (with >30k hits) against 2 million bacterial genomes within 1 minute!
Great pleasure to work with @shenwei356 on a new indexing and alignment scheme, called LexicMap: We have been working on uniformly reassembling, QC-ing and annotating all bacterial (+ now archaeal) data, & wanted to be able to do full alignment to it....
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RT @IgorMartayan: I'm glad to announce that the simd-minimizers library is out! @curious_coding and I have been optimizing the computation…
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RT @curious_coding: I did a project on making an optimized implementation of the S+ tree. The result is 40x speedup over plain binary searc…
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We'll provide an index for AllTheBacteria assemblies on AWS later (next year).
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LexicMap can even index Logan project ( contigs (assemblies of the whole planet), which can be seen as fragmented microbial assemblies💡. LexicMap splits Logan contigs into multiple chunks, and alignments from these chunks are merged after searching.
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RT @AJamesMcCarthy: This is how mass hysteria spreads. A media outlet betraying the trust of their viewers by sharing an out of focus light…
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Sorry again🤦♂️, v0.31.1 brought another bug resulting in wrong results in `filter2/mutate2/mutate3. Please upgrade! `csvtk pretty`: allows customizing max/min width for each column. I used it to generate readable tables for LexicMap results, for users.
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@vircurator @ZaminIqbal Since we recommend >= 200 queries, the precision should not be a problem. Please have a try 😀
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@vircurator I'm not :) Yeah, ICTV is a totally different system. I just converted it to NCBI-format taxdump files.
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RT @gangfang_1: Preprint alert 🚨 Cautions in the use of @nanopore sequencing to map DNA modifications: officially reported “accuracy” ≠ re…
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RT @curious_coding: I gave a talk recently at Ben Langmead's group on my post on fast computation of random minimizers. Was super fun! Blo…
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Amazing!!!
🧬🔍There are 50 petabases of freely-available DNA sequencing data. We introduce "Logan Search" which allows you to search for any DNA sequence in minutes, bringing Earth’s largest genomic resource to your fingertips. 🏔️ 🏔️ #Genomics #Bioinformatics 🧵👇
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RT @BQPMalfoy: I am super excited to share our latest preprint with @yhhshby, @IgorMartayan, and Lucas Robidou on k-mer representations, in…
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