I extracted metagenomic DNA from sediment samples using the PowerSoil kit and performed shotgun sequencing (2×150 bp) on a NovaSeq platform, yielding approximately 40 million high-quality reads per sample. Despite successful quality control, I was unable to generate any bins using MetaWRAP's binning module. What could be the reasons for this binning failure?
Hey there!
What was the N50 of your input assembly? And which assembler and binner options are you choosing? Is there a minimum contig length cutoff used by the binner?
E.g. if your assembly has an N50 of, say, 1500 (i.e. not a great assembly), and the binner has a min contig length cutoff of 3000, you'll be losing a ton of contigs, which could be leading to the lack of bins.
Also, are there any warning or error messages in the log files from MetaWRAP that could hint at what the issue is?
Hi Sushmitha
Binning is allways a tricky part because it really depends on the algorithm used by the binning software. What I consider best is to use more than one (examples MetaBat, Concoct, MixBin, etc.), and then come to a consensus using DasTool. Write me if you need any additional help.
Hi Ricardo Franco-Duarte
I saw a major difference in the N50 of the assembly using SPAdes, wherein N50 was very less ~500-1000. This can be a reason. Is there a way to increase that?
Thanks in advance
Sushmitha T J, try megahit for the assembly. From my experience, it works way better...
Dear Ricardo Franco-Duarte
Megahit has given me lesser N50 than SPAdes.
Sushmitha T J , did you check the total assembly length and the largest contig? Sometimes N50 is worse, but overall the assembly is better. But it really depends on the data, of course. Did you check if you obtain any bins with the megahit assembly?
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