User: chen

gravatar for chen
chen1.5k
Reputation:
1,530
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Location:
OpenGene
Website:
https://github.com/Ope...
Last seen:
1 week, 6 days ago
Joined:
2 years, 8 months ago
Email:
c***@haplox.com

Libraries and tools for NGS data analysis and bioinformatics:

https://github.com/OpenGene

Posts by chen

<prev • 191 results • page 1 of 20 • next >
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Answer: A: Trimmomatic usage issue
... You goal can be achieved by using `sliding window pruning`. You may try [fastp](https://github.com/OpenGene/fastp) with following command: ``` fastp -i Read_1.fq, -I Read_2.fq -o Read_1.out.fq -O Read_2.out.fq -5 -3 -M 28 ``` ...
written 18 days ago by chen1.5k
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Answer: A: Open Source Bioinformatics projects for beginners
... Hi Eugenia84, maybe you will be interested in participating the OpenGene projects: https://github.com/OpenGene Following are some OpenGene projects: - [fastp](https://github.com/OpenGene/fastp): A ultra-fast FASTQ preprocessor with full features (QC/adapters/trimming/filtering/splitting...) - ...
written 11 weeks ago by chen1.5k
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Answer: A: how to adjust phred33 and phred64 in a fastq
... phred64 is out of date, and it's recommended to convert phred64 FASTQ to phred33 FASTQ before downstream analysis. You can google it to find a lot of tools for this conversion. ...
written 3 months ago by chen1.5k
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Comment: C: tumor/normal WGS with CNVkit has many small segments with small copy number chan
... You can post the figure generated by CNVKit. ...
written 3 months ago by chen1.5k
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Answer: A: what cause poly-G from NextSeq
... This is because NextSeq uses a two-colour chemistry system, different from the HiSeq series that use a four-colour system. In the two-colour system: - Green denotes T - Red denotes C - Yellow (Green + Red) denotes A - Black ( No Green, no Red) denotes `G` As the sequencing by synthesis (SBS) ...
written 3 months ago by chen1.5k
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Comment: C: String matching algorithms of biological sequences
... Sorry, but I don't have a library for that. ...
written 3 months ago by chen1.5k
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Answer: A: String matching algorithms of biological sequences
... You may have interest to take a look at the source code of [MutScan](https://github.com/OpenGene/MutScan). MutScan is based on DNA sequence string matching algorithm, and it can detect and visualize target mutations by scanning FastQ files directly. ...
written 3 months ago by chen1.5k
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Answer: A: Faster reading sequences from a fastq file
... You can try the code of [fastp](https://github.com/OpenGene/fastp), which provides ultra-fast FASTQ file preprocessing. You may look into the [src/fastqreader.cpp](https://github.com/OpenGene/fastp/blob/master/src/fastqreader.cpp) which provides a almost-standalone C++ class to read FASTQ file, and ...
written 3 months ago by chen1.5k
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Tool: fastp, the ultra-fast FASTQ preprocessing tool, is now on BioConda
... [fastp](https://github.com/OpenGene/fastp) is a tool designed to provide ultra-fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. # Features: 1. filter out bad reads (too low quality, too short, or too many N... ...
tutorial fastp tool written 3 months ago by chen1.5k
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Comment: C: AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for f
... AfterQC doesn't support multi-threading since it's in Python, you can use another tool I developed, which is much faster and more powerful -- [fastp](https://github.com/OpenGene/fastp) ...
written 3 months ago by chen1.5k

Latest awards to chen

Popular Question 17 days ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Programming language for Computational Biology
Appreciated 11 weeks ago, created a post with more than 5 votes. For A: Good Habit for Bioinformatics Analyst or Scientist
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
Popular Question 4 months ago, created a question with more than 1,000 views. For MutScan: Detect important mutations by scanning FastQ files directly
Scholar 4 months ago, created an answer that has been accepted. For A: How to change the quality score of reads ? (quick help is appreciated)
Appreciated 5 months ago, created a post with more than 5 votes. For MutScan: Detect important mutations by scanning FastQ files directly
Scholar 5 months ago, created an answer that has been accepted. For A: How to change the quality score of reads ? (quick help is appreciated)
Guru 5 months ago, received more than 100 upvotes.
Appreciated 7 months ago, created a post with more than 5 votes. For MutScan: Detect important mutations by scanning FastQ files directly
Appreciated 7 months ago, created a post with more than 5 votes. For MutScan: Detect important mutations by scanning FastQ files directly
Popular Question 7 months ago, created a question with more than 1,000 views. For MutScan: Detect important mutations by scanning FastQ files directly
Centurion 8 months ago, created 100 posts.
Good Question 10 months ago, asked a question that was upvoted at least 5 times. For How to detect CNV with panel sequencing?
Popular Question 11 months ago, created a question with more than 1,000 views. For MutScan: Detect important mutations by scanning FastQ files directly
Popular Question 12 months ago, created a question with more than 1,000 views. For MutScan: Detect important mutations by scanning FastQ files directly
Appreciated 17 months ago, created a post with more than 5 votes. For MutScan: Detect important mutations by scanning FastQ files directly
Popular Question 17 months ago, created a question with more than 1,000 views. For How to detect CNV with panel sequencing?
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Programming language for Computational Biology
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Sudden quality drop in the middle of HiSeq R1 reads but not in R2?
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Sudden quality drop in the middle of HiSeq R1 reads but not in R2?
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: Sudden quality drop in the middle of HiSeq R1 reads but not in R2?
Scholar 2.0 years ago, created an answer that has been accepted. For A: How to change the quality score of reads ? (quick help is appreciated)

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