Hi,
we succesfully sequenced a DNA sample and assembled the genome with canu.
We got one circular contig which is perfect. But the contig is overlapping.
Since nanopore Reads are very long some reads at the end have the same sequence as the reads at the beginning of the contig and vice versa.
Canu is also reporting that the contig is circular.
Now we want to fix those reads at the beginning and the end of the contig to get one linear contig without overlaps.
I cannot find any software to help us there except "circlator". I guess it's the minimus2 function we have to use here, but this function has dependencies to the software AMOS which seems to be impossible to install on Ubuntu 18.04.
Can anyone help us here? Maybe any alternative software to circlator?
Of course we could always trim the contig manually by finding the end of the contig at the beginning and then trim at this position or use a script which does the same... but...the best code is still the one which has already been written by someone else :-)
we succesfully sequenced a DNA sample and assembled the genome with canu.
We got one circular contig which is perfect. But the contig is overlapping.
Since nanopore Reads are very long some reads at the end have the same sequence as the reads at the beginning of the contig and vice versa.
Canu is also reporting that the contig is circular.
Now we want to fix those reads at the beginning and the end of the contig to get one linear contig without overlaps.
I cannot find any software to help us there except "circlator". I guess it's the minimus2 function we have to use here, but this function has dependencies to the software AMOS which seems to be impossible to install on Ubuntu 18.04.
Can anyone help us here? Maybe any alternative software to circlator?
Of course we could always trim the contig manually by finding the end of the contig at the beginning and then trim at this position or use a script which does the same... but...the best code is still the one which has already been written by someone else :-)
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