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Wei Shen 沈伟

Postdoctoral researcher
Institute for Viral Hepatitis, The Second Affiliated Hospital of Chongqing Medical University, China

Github | Twitter | Biostars | Google Scholar | ORCID

  • 🔬 I’m currently working on microbial genomics and metagenomics.
  • 🔭 I'm passionate about reproducible research and open-source software.

Learn more:

I'm grateful to users who have greatly helped to report bugs and suggest new features.
I may respond to issues or fix bugs quickly, but I usually implement new features periodically (two or more weeks).


  1. kmcp Public

    Accurate metagenomic profiling && Fast large-scale sequence/genome searching

    Go 91 7

  2. unikmer Public

    Toolkit for k-mer with taxonomic information

    Go 47 6

  3. seqkit Public

    A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang

    Go 840 122

  4. taxonkit Public

    A Practical and Efficient NCBI Taxonomy Toolkit

    Go 180 20

  5. GTDB taxonomy taxdump files with trackable TaxIds


  6. csvtk Public

    A cross-platform, efficient and practical CSV/TSV toolkit in Golang

    Go 727 72

678 contributions in the last year

May Jun Jul Aug Sep Oct Nov Dec Jan Feb Mar Apr May Mon Wed Fri

Contribution activity

May 2022

Created a pull request in bioconda/bioconda-recipes that received 3 comments

Update TaxonKit to v0.11.1

Describe your pull request here Update TaxonKit to v0.11.1 Please read the guidelines for Bioconda recipes before opening a pull request (PR). If…

+3 −3 3 comments
Opened 1 other pull request in 1 repository
bioconda/bioconda-recipes 1 merged

Created an issue in MoultDB/taxonbridge that received 2 comments

better way to call TaxonKit reformat

Hi, thanks for using TaxonKit in this tool. Since v0.8.0, taxonkit reformat supports input of TaxIds, which is more robust than parsing taxon names…

Opened 2 other issues in 2 repositories
1 contribution in private repositories May 10

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