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User: chen

gravatar for chen
chen • 1.6k
Reputation:
1,620
Status:
Trusted
Location:
OpenGene
Website:
https://github.com/Ope...
Last seen:
3 days, 2 hours ago
Joined:
2 years, 11 months ago
Email:
c***@haplox.com

Libraries and tools for NGS data analysis and bioinformatics:

https://github.com/OpenGene

Posts by chen

<prev • 198 results • page 1 of 20 • next >
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Tool: fastp (the ultra-fast all-in-one FASTQ preprocessing tool) v0.18.0 released, 2X faster, with many new features.
... # fastp An open-source 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. fastp github repo: https://github.com/OpenGene/fastp # features 0. comprehensive quality profiling for both ...
qc fastp filtering tool written 10 days ago by chen • 1.6k • updated 4 days ago by lena1graham • 0
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Comment: C: quality trimming with trimmomatic
... Thank you, Emily. Your suggestion is good. ...
written 9 weeks ago by chen • 1.6k
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Comment: C: gencore: a tool to reduce sequencing noises by generating consensus reads
... gencore supports calling consensus reads with or without UMI. Although UMI is not required, it is strongly recommended. If your FASTQ data has UMI integrated, you can use fastp to shift the UMI to read query names. If your data has no UMI, only mapping position information is used to cluster the ...
written 10 weeks ago by chen • 1.6k
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Answer: A: quality trimming with trimmomatic
... I suggest you to try another quality profiling and trimming tool [fastp](https://github.com/OpenGene/fastp), which is easier to use and is 3x faster than Trimmomatic. ...
written 10 weeks ago by chen • 1.6k
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Answer: A: How to tell when NextSeq, HiSeq, and MiSeq are done?
... I remember there is one file named `*complete*.txt` in the run folder when it's done. ...
written 10 weeks ago by chen • 1.6k
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Comment: C: gencore: a tool to reduce sequencing noises by generating consensus reads
... The reads with same mapping start position and same insert size are clustered first. Then this cluster is divided to different groups by comparing their UMI. By default, for properly mapped reads, the threshold for UMI grouping is 2, and for improperly mapped reads, the threshold is 0. ...
written 10 weeks ago by chen • 1.6k
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Tutorial: gencore: a tool to reduce sequencing noises by generating consensus reads
... `gencore` is a tool to generate consensus reads. It's a new open source project in github: https://github.com/OpenGene/gencore . It is one project developed by [OpenGene](https://github.com/OpenGene) group, which also develops [fastp](https://github.com/OpenGene/fastp), [MutScan](https://github.c ...
consensus sequencing noise tutorial opengene written 10 weeks ago by chen • 1.6k
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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 3 months ago by chen • 1.6k
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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 5 months ago by chen • 1.6k
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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 5 months ago by chen • 1.6k

Latest awards to chen

Popular Question 6 weeks ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
Popular Question 3 months ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Programming language for Computational Biology
Appreciated 5 months ago, created a post with more than 5 votes. For A: Good Habit for Bioinformatics Analyst or Scientist
Popular Question 5 months ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
Popular Question 6 months ago, created a question with more than 1,000 views. For MutScan: Detect important mutations by scanning FastQ files directly
Scholar 7 months ago, created an answer that has been accepted. For A: How to change the quality score of reads ? (quick help is appreciated)
Appreciated 7 months ago, created a post with more than 5 votes. For MutScan: Detect important mutations by scanning FastQ files directly
Scholar 8 months ago, created an answer that has been accepted. For A: How to change the quality score of reads ? (quick help is appreciated)
Guru 8 months ago, received more than 100 upvotes.
Appreciated 10 months ago, created a post with more than 5 votes. For MutScan: Detect important mutations by scanning FastQ files directly
Appreciated 10 months ago, created a post with more than 5 votes. For MutScan: Detect important mutations by scanning FastQ files directly
Popular Question 10 months ago, created a question with more than 1,000 views. For MutScan: Detect important mutations by scanning FastQ files directly
Centurion 11 months ago, created 100 posts.
Good Question 12 months ago, asked a question that was upvoted at least 5 times. For How to detect CNV with panel sequencing?
Popular Question 14 months ago, created a question with more than 1,000 views. For MutScan: Detect important mutations by scanning FastQ files directly
Popular Question 14 months ago, created a question with more than 1,000 views. For MutScan: Detect important mutations by scanning FastQ files directly
Appreciated 19 months ago, created a post with more than 5 votes. For MutScan: Detect important mutations by scanning FastQ files directly
Popular Question 19 months ago, created a question with more than 1,000 views. For How to detect CNV with panel sequencing?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Programming language for Computational Biology
Appreciated 21 months ago, created a post with more than 5 votes. For AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
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?
Appreciated 2.2 years ago, created a post with more than 5 votes. For AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Teacher 2.2 years 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 2.2 years 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?
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