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I am working with a data set that uses flow pattern b and hence, Qiime and AmpliconNoise cannot be used for the denoising step:
"Since late 2012, 454 machines have a new feature (flow pattern B) that is supposed to allow for longer reads. Unfortunately, files using this feature can not be denoised, but result in nonsense output."
"Not sure how ampliconnoise or Acacia behave, but a simple grep over ampliconnoise's code base showed several hardcoded occasions of the regular flow order TACG, so I assume that it might have some issues as well."
Non-flow based denoiser such as Acacia or FlowClus overcome that obstacle, however they only generate a fasta file as an output. For my analysis, a fastq file would be needed. Are some tools available that both cope with flow pattern b AND generate a fastq file?
"Since late 2012, 454 machines have a new feature (flow pattern B) that is supposed to allow for longer reads. Unfortunately, files using this feature can not be denoised, but result in nonsense output."
"Not sure how ampliconnoise or Acacia behave, but a simple grep over ampliconnoise's code base showed several hardcoded occasions of the regular flow order TACG, so I assume that it might have some issues as well."
Non-flow based denoiser such as Acacia or FlowClus overcome that obstacle, however they only generate a fasta file as an output. For my analysis, a fastq file would be needed. Are some tools available that both cope with flow pattern b AND generate a fastq file?