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What tool can align a ton of NGS data from a large region to a tiny reference? Gingeneticist Bioinformatics 4 01-06-2014 03:35 AM

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Old 09-25-2015, 06:53 AM   #1
mido1951
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Location: Tunisia

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Default tool for filtering NGS data

Hello,
I want to do a cleaning of my data (short and long reads reads) to minimize the error rate.
i have data (short and long reads) from diffrent plaeforms and this data are very noisy and I want to clean them for my experiments.

Do you suggest me good cleaning tools?
Thank you
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Old 09-25-2015, 07:01 AM   #2
GenoMax
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BBduk.sh (from BBMap), Trimmomatic, Cutadapt are all great tools for trimming NGS data based on scanning for adapter presence, quality scores, length etc. They all have individual threads on SeqAnswers.

BTW how did you decide that your data is noisy?
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Old 09-25-2015, 07:55 AM   #3
mido1951
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I did some research and found QCtoolkit. What do you think of this tool?
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Old 09-25-2015, 07:59 AM   #4
GenoMax
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Many tend to use FastQC for NGS data QC. FastQC is user friendly and can handle many types of NGS data. Give that a try as well.
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