With the aim to find special genomic functions we have sequenced metagenomic DNA using Illumina Hiseq. As this method gives the raw data in FastQ format we need to verify the quality before acceding to the mapping and data analysis. are there any works or articles which compare between different platforms and workflows in order to find the best way to achieve our goal?
Hi Farah,
MetaGeneMark software is useful for detection of ORFs, CD-HIT-EST software will help to create a non-redundant set of ORFs. Microbial traits could be assessed and identified with software and databases as GOTTCHA (Genomic Origins Through Taxonomic Challenge) and KEGG (Kyoto Encyclopedia of Genes and Genomes).
Regards,
Thank you very much Zayda Morales Moreira for the reply.
For MetaGeneMark and CD-HIT-EST are for FASTA format only if I am not mistaken.
In our research we are doing functional analysis (looking for special enzymes) not for taxonomic analysis, this is the difference between function based metagenomic (what we are doing) and sequence based metagenomic . so are there other options?
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