Correction of sequencing error using only Bowtie?

Question

[andres.firrincieli]

Dear All,

I was reading an old paper published on Nucleic Acid Research about the sequencing of a bacterial genome. The authors performed a primary assembly using 454 reads (36 coverage), and the resulting contigs were scaffolded using a jumping library with an average insert size of 3 kb. The authors also did an Illumina sequencing (400X coverage), and the reads were used as follow:

Illumina reads (300 bp) were mapped to this assembled whole genome sequence to identify potential single miss-called nucleotides using the Bowtie method

As far as I know, the "bowtie method" does not correct for sequencing errors, and the method used to correct the errors introduced by the 454 reads is not mentioned in the paper.

Did I miss somenthing? Can we use bowtie alone to correct for sequencing errors?

Thanks!

ps. Sequencing reads are not available in SRA

link to the paper

[seidel]

Wouldn't the CIGAR string of a bowtie alignment indicate non-matching bases? i.e. "potential single miss-called nucleotides". Though I would imagine if they did this they would hopefully mention custom scripts to parse the information.

Answer 1

[colindaven]

No.

They probably mean manual correction of errors after SNP calling on the BAM files. Back then, tools like Pilon/Racon for automated correction did not exist (as far as I remember).

The methods are very poor, you're quite correct.