Tweet
Software suggestions for novel genomes?
Hi all,
We recently got a bunch of putative novel contigs from a metagenome analysis (basically just sequenced the heck out of human blood). We have a bunch of contigs 2-15kb in length from multiple different individuals containing reads that don't align to any of the known genomes (bacterial, viral, human).
I have picked a few of these contigs, looked for ORFs and performed BLASTX searches to see what is in there. Performing these (not exactly high-throughput...) analyses, I can see that some of these contigs appear to come from novel bacteria that are distantly related to known ones. Now, the question is - how do I scale this analysis up? I have been looking at MEGAN and METAREP and think maybe the latter is more suitable - but appears to be almost impossible to work with for a mare mortal. Any comments or other suggestions would be very helpful.
Thanks in advance.
We recently got a bunch of putative novel contigs from a metagenome analysis (basically just sequenced the heck out of human blood). We have a bunch of contigs 2-15kb in length from multiple different individuals containing reads that don't align to any of the known genomes (bacterial, viral, human).
I have picked a few of these contigs, looked for ORFs and performed BLASTX searches to see what is in there. Performing these (not exactly high-throughput...) analyses, I can see that some of these contigs appear to come from novel bacteria that are distantly related to known ones. Now, the question is - how do I scale this analysis up? I have been looking at MEGAN and METAREP and think maybe the latter is more suitable - but appears to be almost impossible to work with for a mare mortal. Any comments or other suggestions would be very helpful.
Thanks in advance.