how to align fastq files to a fasta file using biopython to produce VCF file

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3.4 years ago

FadyNabil ▴ 20

I have many fastq files that I want to align to a fast file using biopython package

fastq biopython fasta VCF • 2.2k views

ADD COMMENT • link updated 3.4 years ago by Ram 44k • written 3.4 years ago by FadyNabil ▴ 20

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Using biopython for this task is unlikely to be the best approach, can you elaborate why you want to do that?

ADD REPLY • link 3.4 years ago by WouterDeCoster 47k

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I am running on a project that needs me to make alignment for fastq files

ADD REPLY • link 3.4 years ago by FadyNabil ▴ 20

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Yes, but BioPython is not what you want. Alignment of fastq files (NGS sequencing data, is it?) is done with specialized tools such as bwa or bowtie2. Please google for these tools, there are literally hundreds of posts, tutorials and manuals on how to do that. The entire process is called variant calling, there are pipelines for it, please search for these. Something like GATK best practices or bcftools mpileup as good keywords to start with.

ADD REPLY • link 3.4 years ago by ATpoint 85k

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I got it thank you

ADD REPLY • link 3.4 years ago by FadyNabil ▴ 20

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So what is the problem, you opened a new question? Feel free to add a comment if you need further help. Did you get stuck somewhere, if so where? There is no need to be ashamed asking for help, but please do not just open identical questions, that only annoys people :)