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However, scaffolds are nothing but a combination of contigs filled with "estimates" of gaps in between. Does that not mean then that it is more sensible to compare contigs than to compare scaffolds as it has estimate of gaps in between which may be highly erroneous! -
Compare Genomes
I suppose it depends what your question is.
But, typically the goal of genome assembly is to create one scaffold per chromosome (assemble the entire genome/chromosome). With this in mind, I think it would make more sense to compare scaffolds to scaffolds.Leave a comment:
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But is it good to use the contigs files or to use the scaffolds files for comparison?Leave a comment:
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De novo to reference comparison
I have had good luck with both MUMmer and MAUVE.
MAUVE is very straight forward and MUMmer I simply follow the recipes in the manuel.Leave a comment:
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For mammalian genomes, use bwa-sw. Two human assemblies in several CPU days.Leave a comment:
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Use NUCmer from the MUMmer package (available from Sourceforge.) For large reference genomes, you have to split the reference into smaller pieces for it to fit in memory, then align everything to those pieces. It is relatively fast and efficient, and seems to be a commonly used tool as the basis for other assembly comparison pipelines. There are some recently available wrapper scripts which automate some of the steps, but it's not tough to run through the steps yourself. The online docs for MUMmer as a whole are very good.Leave a comment:
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Compare Genomes
Hi everyone, I did Genome assembly by SOAPdenovo and obtained contigs and scaffolds, now I wanna compare these scaffolds to some reference genomes downloaded from Genbank. I am wondering what tools I can use to do this job, I used BLAST but it is not in good visualization, any other advice on such tools and programs?
I am new to this, any suggestion is appreciated.
Thanks
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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