User: chen
chen • 1.7k
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Libraries and tools for NGS data analysis and bioinformatics:
Posts by chen
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... 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
chen • 1.7k
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190
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... Thanks, I will do the benchmark and post the results. ...
written 6 weeks ago by
chen • 1.7k
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190
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6 follow
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... `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 ...
written 6 weeks ago by
chen • 1.7k
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... # 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 ...
written 11 weeks ago by
chen • 1.7k
• updated
10 weeks ago by
lena1graham • 0
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Comment:
C: quality trimming with trimmomatic
... Thank you, Emily. Your suggestion is good. ...
written 4 months ago by
chen • 1.7k
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427
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... 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
chen • 1.7k
1
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2
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826
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... 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
chen • 1.7k
0
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2
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409
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... I remember there is one file named `*complete*.txt` in the run folder when it's done. ...
written 4 months ago by
chen • 1.7k
1
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427
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... 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
chen • 1.7k
3
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427
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... `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 ...
written 4 months ago by
chen • 1.7k
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