Sanger sequencing ab1 file Alignment and variant calling
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6.0 years ago

Hello All, I am looking for the aligner other than BWA I have fastq file as input and expected outfile is sam format and reference is rCRS fasta file n even suggest the best variant calller for the same protocol.

genome sequencing • 2.2k views
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Why do you have sanger/ab1 file reference in title and a question about fastq files in the body of the post? Please clarify/reconcile those two things.

There are plenty of other aligners (besides BWA) that can fit that bill.

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Sir, i get the ab1 file from machine so with the help of phred i generate the fastq file . so is it possible to do alignment directly by ab1 even by fastq

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You generated file(s) for ab1 sequences that look like fastq where you are using ASCII encoded phred scores that came from original sanger call?

Would you mind commenting on why you are following this round about way for what must be a small number of reads (relatively, if they are ab1)? Can't you use your ab1 files directly for variant calls?

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Sir here is a small flowchart of my workflow get the ab1 file from sequencer -> do the quality trimming by phred and generate fastq file using perl -> do the alignment with rCRS fasta file get the sam file -> convert sam to bam and call variants using variant caller. and do the annotation by annovar but i m not getting the 3243 MELAS common mutation in it , my protocol is not able to detect the variants . so can u help me

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