Question: Adapters trimming for non-ILLUMINA data?

OpenGene / fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

MIT License

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Question: Adapters trimming for non-ILLUMINA data? #107

Open Zjianglin opened 5 years ago

Zjianglin commented 5 years ago

Dear developers,

I am a bioinformatics student, and I plan to perform QC for many NGS reads data from several different sequencing platforms such as ILLUMINA, LS454, ION_TORRENT, and ABI_SOLID. Your excellent paper and AfterQC said that Currently it supports processing data from HiSeq 2000/2500/3000/4000, Nextseq 500/550, MiniSeq...and other Illumina 1.8 or newer formats. I wonder if there is any method to perform adapters trimming for non-ILLUMINA data?

Thanks, and I'm looking forward to your reply.

sfchen commented 5 years ago

I think it supports most non-ILLUMINA data. You can post your data (just some reads with adapters) if don't whether it can do, then we can take a look at your data.

Zjianglin commented 5 years ago

Thans for your reply. I downloadefd thousands of SRA from NCBI and I want to perform a preprocess QC on these SRAs for further analysis. Actually I don't know if one reads with adapters or not. So as you said, could I just preform fastp process for all these reads?

sfchen commented 5 years ago

I think you can. If you have any problem, just let me know.

Zjianglin commented 5 years ago

Okay, Thank you~