hi all , what is the approximate total number of contigs we should get in a velvet assembly? I would like to know this because i did assemblies with various parameters but i always get more then million contigs..
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Use VelvetOptimizer.pl
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In a genomic assembly you should get exactly the number of chromosomes for that species or you've made a horrible mistake.
Seriously, i think you are beginning to shoot from the hip with your questions to this board. Post some more specifics or do some research on your own.Comment
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What are you trying to assemble?
Here are some numbers from CLCbio tool: http://www.clcbio.com/index.php?id=1413
Lesser, longer contigs are better, provided they are not incorrect!--
bioinfosmComment
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hello zingster ..iam very new to this kind of research and iam not expertise like you in bioinfo ....so only i have these kind of questions araises..im sry if iam hard..Comment
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This thread reminds me of something...thanks...(will post the idea in the Site Feedback forum shortly...)Comment
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Searching in the dark
Yes, it's better we know the exact chr number. But not all the organisms we know their chromosome. A good way is to align to a closely related organism and then to check the left contigs.
Originally posted by Zigster View PostComment
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Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
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