Tool For Taxonomy Classification Of contigs and reads

Question

[blancai.taboada]

Hello all,

I have assembled (using IDBA) illumina contigs for taxonomic classification. Is there any tool which can do the taxonomic classification of assembled illumina reads.

I used Megan in order to analyze data generated using blastn from both, contigs and reads that we were not able to ensemble. How can this be reflected in MEGAN or other tool? For example in the header id of contigs I know how many reads are used

headerId_readsUsedforContig

and for the reads I have

headerId_1.

I want to consider this information for example for compare samples and for rarefaction, shannon index, etc.

As I said, I tried MEGAN. But MEGAN is only considering the read counts.

Please give me some advise here.

Best regard,

Blanca

Answer 1

[Brian Bushnell]

BBSketch does taxonomic classification of contigs or reads. However, it does not weight contigs by the number of reads used; that sounds like a job for a custom program.

Answer 2

[Sej Modha]

You can use DIAMOND to classify sequences and then convert the accession to taxonomy ID.

[bird77]

Hi Sey, sorry, found the thread much much later. I have protein fasta files which I want to classify. Can you tell me how DIAMOND is used for that? I am not clear about what to use as reference sequence. Thank you.

Answer 3

[bioinfoSeeker]

CLARK can be used for taxonomic classification of assembled reads.