Blast run for de novo assembly analysis using command line

Question

[sauravzoology88]

I would like to know how to run the BLAST using windows command line. Kindly anyone tells me the command line which helps me for this purpose. Thanks

[Joe]

Don’t use the windows command line. It’s essentially impossible to get any real bioinformatics done that way.

A reasonable compromise is the Linux Subshell for Windows. Start with that, and then come back to us with any more specific questions about running BLAST and the data you have.

[ATpoint]

Hi sauravzoology88,

please use google and the search function here for these kind of things. There are multiple threads on this, and additionally the extensive documentation on NCBI. Spend some quality time on the manual, and consider to abandon Windows for Linux ;-D

[GenoMax]

In theory/practice (with right hardware) it is possible to do this BLAST on windows but can you tell us what hardware configuration you have access to? I am going to assume that you have assembled a genome and now want to find out what is there and where. To do the search against nt ot nr is going to need a lot of RAM unless you are only interested in a specific genome/set of organisms.