how to align many single end fastq files from the same study on each other without using any reference genome using python?
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15 months ago
FadyNabil ▴ 10

I have many single end fastq files that I downloaded from SRA data base I want to align these files on each other to make a consensus genome that I will consider it as my reference genome how can I make this alignment by using python?

fastq fasta python VCF • 650 views
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I want to align these files on each other to make a consensus genome

That is not how you create a consensus for a genome. You would either need to align to a reference and/or assemble the data.

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but is there is a way to make alignment on these files without using ref genome by using python?

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Aligning millions of fastq reads to each other makes no logical sense. python is a programming language not a tool for analysis.

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15 months ago
JC 13k

That is called genome assembly, not alignment, also python is not used for that. Check assembly tools such as SPAdes.

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