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Old 12-01-2016, 06:22 AM   #43
bavci
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Location: Bremen, Germany

Join Date: Dec 2016
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I just saw this comment from Brian Bushnell:

P.S. DO NOT use read-extension or error-correction for metagenomic 16S or other amplicon studies! It is intended only for randomly-sheared fragment libraries. Error-correction or read-extension using any algorithm are a bad idea for any amplicon library with a long primer. For normal metagenomic fragment libraries, these operations should be useful and safe if you specify a sufficiently long K.

I recently used Tadpole for contig extension. After reading this comment, I am not sure Tadpole is a reliable tool for this. I have full-length 16S rRNA gene sequences from clone libraries. I took the variable region of 16S rRNA gene sequences (first 300 nt nucleotides) and mapped on metagenome contigs which are taxonomically classified as taxa of interest. These metagenome contigs were assembled from randomly-sheared metagenomic fragment libraries (sequencing platfrom: HiSeq). 300 nt nucleotide of 16S rRNA gene sequence perfectly mapped on a contig. I then run Tadpole to extend this contig using all pair-end reads in this metagenome. I could extend the contig up to 6500 nucleotide.

Is Tadpole reliable for such usages?
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