Building multiple consensus sequences from multiple fasta sequences

Question

[miss]

I am new to NGS data analysis and I don't know how to overcome this problem: I have DNA-seq results from 12 different sites stored in one fasta file. Approximately every site has around 1000 reads, so I have 12000 reads in file but I don't know to which site any read belongs. I should build consensus sequences for all 12 sites without having reference sequence or knowing which reads belong to which site. Is it possible to do it and if yes, how?

[doppelganger1030]

Hallo, I have similar problems. I have 96 fastq files and I performed alignment on them. On average I have about 30 fastq files aligned to the RefSeq database built. The outputs of the alignment were .fasta and .sam files. I want to generate a consensus sequence from them. How best can this be done?

Answer 1

[Jean-Karim Heriche]

An approach that doesn't require any prior knowledge is to cluster the sequences based on all pairwise sequence similarities/distances then compute a multiple sequence alignment for each cluster. Refinements can be made based on how much extra information is available.

[miss]

Thank you! Any software tool you can recommend me for this kind of clustering?

[Jean-Karim Heriche]

You'll need to identify which sequence alignment algorithm is relevant for your sequences, run the similarity computations in parallel then apply a clustering algorithm to the resulting distance or similarity matrix. All this can be done with a bit of scripting in your favourite language.