User: shenwei356

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shenwei3563.1k
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3,120
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Location:
China
Website:
http://shenwei.me/
Twitter:
shenwei356
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Google Scholar Page
Last seen:
3 hours ago
Joined:
5 years, 2 months ago
Email:
s*********@gmail.com

Wei Shen is a PhD student of Microbiology studying Bioinformatic algorithm and gut metagenomics at Third Military University, China.

He develops and shares many reusable open-source tools on Bioinformatics and data manipulations on Github (http://bioinf.shenwei.me). And he also likes writing posts on software development and scientific research.

Learn more: Google Scholar | ResearchGate | ORCIDGithub.

Posts by shenwei356

<prev • 389 results • page 1 of 39 • next >
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Answer: A: Snakemake vs. Nextflow: strengths and weaknesses
... [Table 1: Comparison of Nextflow with other workflow management systems](https://www.nature.com/nbt/journal/v35/n4/fig_tab/nbt.3820_T1.html) Workflow Nextflow Galaxy Toil Snakemake Bpipe Platforma Groovy/JVM Python Python Python Groovy/JVM Native task supportb Yes (any) No No Yes (BASH only) ...
written 3 days ago by shenwei3563.1k
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Answer: A: Column Regex Find And Replace
... [csvtk](https://github.com/shenwei356/csvtk/), supporting Windows/Linux/Mac OS X csvtk replace -H -t -f 2 -p "gi\|(\d+).+" -r "\$1" data.tsv ...
written 4 days ago by shenwei3563.1k
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Comment: C: How do I access genome coverage using SPADES?
... Thanks for your explanation. ...
written 11 days ago by shenwei3563.1k
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Comment: C: extract list of positions from fasta file biopython
... Steps: 1. read the positions as list 1. iterate FASTA records: for seq_record in SeqIO.parse(query_file, "fasta"): for x in positions: # get the base at position x seq_record.seq[x-1] ...
written 14 days ago by shenwei3563.1k
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Answer: A: Collect quality information from raw sequencing data
... [MultiQC](http://multiqc.info/) - Aggregate results from bioinformatics analyses across many samples into a single report ...
written 18 days ago by shenwei3563.1k
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Answer: C: Eutils: identifying complete genomes
... [Manipulation on NCBI refseq bacterial assembly summary](http://blog.shenwei.me/manipulation-on-ncbi-refseq-bacterial-assembly-summary/) ...
written 18 days ago by shenwei3563.1k
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Comment: C: fasta file to tab delimited file
... [seqkit](https://github.com/shenwei356/seqkit) seqkit tab2fx xxx.tab > xxx.fasta ...
written 21 days ago by shenwei3563.1k
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Answer: A: I have DNA motifs 6-12 bp long. Trying to get conservation measurements for them
... For locating motifs, try `locate` command ([usage](http://bioinf.shenwei.me/seqkit/usage/#locate)) of [SeqKit](https://github.com/shenwei356/seqkit). For some motifs: $ cat motifs.txt ACTNGCT GCTGRTCGAAC Convert to FASTA format which seqkit wants: $ awk '{print ">"$1"\n"$1}' ...
written 22 days ago by shenwei3563.1k
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Answer: A: Pattren counter in fasta file
... You can also try [SeqKit](https://github.com/shenwei356/seqkit). $ seqkit locate -p CAGAT seqs.fa | column -t seqID patternName pattern strand start end matched chr1 CAGAT CAGAT + 6 10 CAGAT chr1 CAGAT CAGAT + 24 28 CAGAT ch ...
written 23 days ago by shenwei3563.1k
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Answer: A: Fetching NCBI ID for a list of species?
... try [taxonkit](https://github.com/shenwei356/taxonkit), providing single binary files for Windows/Linux. It's really fast. $ cat names.txt Homo sapiens Akkermansia muciniphila ATCC BAA-835 Akkermansia muciniphila Mouse Intracisternal A-particle Wei Shen uncultured murin ...
written 23 days ago by shenwei3563.1k

Latest awards to shenwei356

Teacher 3 days ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 10 days ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Scholar 15 days ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 21 days ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Teacher 23 days ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 4 weeks ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Scholar 5 weeks ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 6 weeks ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Scholar 7 weeks ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Scholar 7 weeks ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Scholar 9 weeks ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 9 weeks ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Good Answer 11 weeks ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics software distribution
Scholar 11 weeks ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 12 weeks ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 3 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Scholar 3 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Scholar 3 months ago, created an answer that has been accepted. For A: looking for 16S RNA sequence consensus
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: single line fasta to mult line fasta
Appreciated 3 months ago, created a post with more than 5 votes. For C: Inserting delim between numbers and strings in bash

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