User: chen

gravatar for chen
chen1.7k
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1,690
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Trusted
Location:
OpenGene
Website:
https://github.com/Ope...
Last seen:
1 month ago
Joined:
3 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 • 201 results • page 1 of 21 • next >
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Comment: C: Can two mates have different file size?
... Read2 is usually bigger than read1 due to its quality is usually lower than read1, which decreases the compression ration. If you want to check whether the PE files are consistent, you can use a tool called PE check: https://github.com/OpenGene/pecheck ...
written 5 weeks ago by chen1.7k
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Comment: C: repaq: compress Illumina FASTQ to be as small as 1/4 of the gzip format.
... Thanks, I will do the benchmark and post the results. ...
written 6 weeks ago by chen1.7k
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Tool: repaq: compress Illumina FASTQ to be as small as 1/4 of the gzip format.
... `repaq` is an open source tool for FASTQ compression: https://github.com/OpenGene/repaq It repacks Illumina format FASTQ to a smaller binary file (.rfq), which can be further compressed by xz or pxz (.rfq.xz). For NovaSeq data, the .rfq file can be much smaller than .fq.gz, and the compressing ...
compress repaq fastq tool written 6 weeks ago by chen1.7k
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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 11 weeks ago by chen1.7k • updated 10 weeks ago by lena1graham0
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Comment: C: quality trimming with trimmomatic
... Thank you, Emily. Your suggestion is good. ...
written 4 months ago by chen1.7k
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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 4 months ago by chen1.7k
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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 4 months ago by chen1.7k
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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 4 months ago by chen1.7k
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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 4 months ago by chen1.7k
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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 4 months ago by chen1.7k

Latest awards to chen

Popular Question 4 weeks ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: Good Habit for Bioinformatics Analyst or Scientist
Popular Question 3 months ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
Popular Question 5 months ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Programming language for Computational Biology
Appreciated 7 months ago, created a post with more than 5 votes. For A: Good Habit for Bioinformatics Analyst or Scientist
Popular Question 7 months ago, created a question with more than 1,000 views. For Why blast result gives Homo sapiens BAC clone
Popular Question 9 months ago, created a question with more than 1,000 views. For MutScan: Detect important mutations by scanning FastQ files directly
Scholar 9 months ago, created an answer that has been accepted. For A: How to change the quality score of reads ? (quick help is appreciated)
Appreciated 10 months ago, created a post with more than 5 votes. For MutScan: Detect important mutations by scanning FastQ files directly
Scholar 10 months ago, created an answer that has been accepted. For A: How to change the quality score of reads ? (quick help is appreciated)
Guru 10 months ago, received more than 100 upvotes.
Appreciated 12 months ago, created a post with more than 5 votes. For MutScan: Detect important mutations by scanning FastQ files directly
Appreciated 12 months ago, created a post with more than 5 votes. 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
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Good Question 15 months ago, asked a question that was upvoted at least 5 times. For How to detect CNV with panel sequencing?
Popular Question 16 months ago, created a question with more than 1,000 views. 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 MutScan: Detect important mutations by scanning FastQ files directly
Appreciated 22 months ago, created a post with more than 5 votes. For MutScan: Detect important mutations by scanning FastQ files directly
Popular Question 22 months ago, created a question with more than 1,000 views. For How to detect CNV with panel sequencing?
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Programming language for Computational Biology
Teacher 2.1 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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