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User: chen

gravatar for chen
chen • 2.1k
Reputation:
2,080
Status:
Trusted
Location:
OpenGene
Website:
https://github.com/Ope...
Last seen:
3 months ago
Joined:
5 years, 1 month ago
Email:
c***@haplox.com

Libraries and tools for NGS data analysis and bioinformatics:

https://github.com/OpenGene

Posts by chen

<prev • 219 results • page 1 of 22 • next >
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Answer: A: Repost: Quality of RNA Seq Data
... Is it paired-end data or single-end data? Probably you can try [fastp][1] for quality pruning. [1]: https://github.com/OpenGene/fastp ...
written 3 months ago by chen • 2.1k
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Tutorial: A very simple way to detect viruses and microorganisms from mNGS FASTQ data using fastv
... `fastv` is an ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. It detects microbial sequences from FASTQ data, generates JSON reports and visualizes the result in HTML reports. This tool can be used to detect viral infectious diseases, like COVID-19. This too ...
viruses covid-19 sars-cov-2 tutorial fastv written 4 months ago by chen • 2.1k
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Tutorial: introduce a tool for fast identification of SARS-CoV-2 and other microbes from sequencing data
... `NEW: fastv 0.6.0 released, which supports scanning a KMER collection file that contains KMERs of many microorganisms.` fastv is an ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. It detects microbial sequences from FASTQ data, generates JSON reports and vi ...
covid-19 fastv tutorial sars-cov-2 written 5 months ago by chen • 2.1k
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Comment: C: Do you need a deduplication tool for FASTQ data in fastp?
... Thanks for your advice. ...
written 15 months ago by chen • 2.1k
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Comment: C: Do you need a deduplication tool for FASTQ data in fastp?
... Thanks, I will consider your suggestion. For deduplication, I think I can control the RAM usage to be less than 16G for processing even 1Tbp Illumina PE data. ...
written 15 months ago by chen • 2.1k
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Forum: Do you need a deduplication tool for FASTQ data in fastp?
... Hi, I am the author of [fastp][1], a tool to provide ultra-fast all-in-one FASTQ preprocessing functions. This tool has received 500+ stars in github (https://github.com/OpenGene/fastp), and has been cited for 40+ times since its [paper][2] published in Bioinformatics about 8 months ago. Now I am ...
forum fastp deduplication written 15 months ago by chen • 2.1k • updated 8 months ago by manekineko • 130
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Answer: A: Find illumina adaptors
... Normally they are Illumina TruSeq adapters. If you don't know it, use [fastp][1] to detect the adapters automatically. See https://github.com/OpenGene/fastp#adapters for details. Remind to enable `--detect_adapter_for_pe` option if your nextseq 500 data is paired-end. [1]: https://github.com/ ...
written 16 months ago by chen • 2.1k
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Answer: A: How to blast a paired end fastq file?
... You can use [fastp][1] to merge it first, then blast the merged reads See the intro here: https://github.com/OpenGene/fastp#merge-paired-end-reads [1]: https://github.com/OpenGene/fastp ...
written 16 months ago by chen • 2.1k
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Comment: C: help in Language
... If you only want one language, then go with Python first. ...
written 16 months ago by chen • 2.1k
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Comment: C: very confused with GC bias
... Some sequencers, like Illumina NovaSeq may have polyG in end of reads, which may affect GC curve. Use fastp to trim polyG and check the post-filtering data. ...
written 16 months ago by chen • 2.1k

Latest awards to chen

Great Question 3 months ago, created a question with more than 5,000 views. For AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Popular Question 3 months ago, created a question with more than 1,000 views. For MutScan: Detect important mutations by scanning FastQ files directly
Great Question 4 months ago, created a question with more than 5,000 views. For AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Popular Question 4 months ago, created a question with more than 1,000 views. For MutScan: Detect important mutations by scanning FastQ files directly
Appreciated 5 months ago, created a post with more than 5 votes. For A: Good Habit for Bioinformatics Analyst or Scientist
Popular Question 9 months ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
Great Question 9 months ago, created a question with more than 5,000 views. For AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Popular Question 14 months ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
Student 14 months ago, asked a question with at least 3 up-votes. For Is there any C API documentation for HTSLIB?
Popular Question 15 months ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
Popular Question 16 months ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: How to add read depth to gene of my interest
Popular Question 17 months ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: How to add read depth to gene of my interest
Appreciated 20 months ago, created a post with more than 5 votes. For A: Good Habit for Bioinformatics Analyst or Scientist
Popular Question 22 months ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Is there any C API documentation for HTSLIB?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
Appreciated 2.2 years ago, created a post with more than 5 votes. For A: Good Habit for Bioinformatics Analyst or Scientist
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Programming language for Computational Biology
Appreciated 2.6 years ago, created a post with more than 5 votes. For A: Good Habit for Bioinformatics Analyst or Scientist
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