Question: Tool For Taxonomy Classification Of contigs and reads
0
gravatar for blancai.taboada
2.0 years ago by
blancai.taboada0 wrote:

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

ADD COMMENTlink modified 2.0 years ago by Brian Bushnell16k • written 2.0 years ago by blancai.taboada0
2
gravatar for Brian Bushnell
2.0 years ago by
Walnut Creek, USA
Brian Bushnell16k wrote:

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.

ADD COMMENTlink written 2.0 years ago by Brian Bushnell16k
0
gravatar for Sej Modha
2.0 years ago by
Sej Modha4.2k
Glasgow, UK
Sej Modha4.2k wrote:

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

ADD COMMENTlink written 2.0 years ago by Sej Modha4.2k

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.

ADD REPLYlink written 16 months ago by bird7730
0
gravatar for bioinfoSeeker
2.0 years ago by
United Kingdom
bioinfoSeeker20 wrote:

CLARK can be used for taxonomic classification of assembled reads.

ADD COMMENTlink written 2.0 years ago by bioinfoSeeker20
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