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Post Genome Improvement

Can anyone suggest me which tool should I use to improve the contig of four strains of S.aureus. the given contigs are from single end...

Thank u..:)

next-gen genome-sequence assembly
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updated by Ram Ram • written by div • div

improve what?

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written by dago dago

to improve my contigs of four strains....:)

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updated by Ram Ram • written by div • div

2 answers

I would recommend Pilon, from the Broad institute. It is especially suited for the microbial de novo assemblies.

You can also try PAGIT (a little old), for improving assembly.

There might be many more, but these are the ones that I've used and found it quite useful.

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updated by Ram Ram • written by arnstrm arnstrm

I have already used PAGIT but it takes paired end as an input and my contigs are from single end.

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written by div • div

Taking into account the many years we spent trying to to complete (read close) our Pseudomonas genome, I would suggest you to gain time by using PacBio sequencing

You don't mention how long are your single ends, the quality of your reads...

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written by Antonio R. Franco Antonio R. Franco

PacBio sequencing does it improve the contigs with high accuracy.

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written by div • div

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