Handle Sanger ABI file: TraceTuner and Lucy

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11-18-2009, 10:39 AM	#1
AppleInformatics Junior Member Location: WNY Join Date: Nov 2009 Posts: 5	.abi to fasta/fastq conversion script/program? Hi All, We have sanger sequencing data we'd like to incorporate into a de novo 454 bacterial genome assembly using MIRA; only the core facility that does our sanger sequencing can only provide us .abi files, not the more useful fasta/fastq file combination. Any suggestions for a program or script that has useful batch conversion features?

11-19-2009, 03:26 AM

#2

sklages Senior Member Location: Berlin, DE Join Date: May 2008 Posts: 477

Hi, in general it is always better to have the original run/chromatogram data You should basecall the data (not only extracting the sequence from the abi file). There are two (common) basecalling programs: 1) phred (http://www.phrap.org/consed/consed.html#howToGet) 2) TraceTuner (https://sourceforge.net/projects/tracetuner/) Both produce sequences in fasta format with qualities ... You should also get rid of vector / low quality. For sanger data lucy is doing a good job (https://sourceforge.net/projects/lucy/). After basecalling and vector/lowquality clipping you can go for MIRA .. cheers, Sven