User: chen
chen • 1.5k
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Libraries and tools for NGS data analysis and bioinformatics:
Posts by chen
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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
chen • 1.5k
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... 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
chen • 1.5k
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... phred64 is out of date, and it's recommended to convert phred64 FASTQ to phred33 FASTQ before downstream analysis.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
chen • 1.5k
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1
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... You can post the figure generated by CNVKit. ...
written 3 months ago by
chen • 1.5k
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... 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
chen • 1.5k
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3
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... Sorry, but I don't have a library for that. ...
written 3 months ago by
chen • 1.5k
1
vote
3
answers
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... 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
chen • 1.5k
1
vote
5
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5
answers
... 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
chen • 1.5k
6
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... [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... ...
written 3 months ago by
chen • 1.5k
0
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... 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
chen • 1.5k
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