Hi,
I´m searching for a commandline tool to perform a quick pseudoassembly (i. e. mapping of assembled genomic contigs to a reference, ordering of contigs accordingly and filling of gaps with Ns).
Best,
Chris
Is there any way to use ABACAS for this without concatenating the reference genome into a single FASTA file? I was going to use ABACAS for this awhile back but it just got too messy dealing with the huge, unwieldy concatenated output.
Thanks, ABACAS did a good job.
In my case we are just resequencing a bacterial genome that had already been sequenced some years ago. So, the difference between our sequences is less than 1%.
I would think that ABACAS does not perform well on more distant or complex genomes.
Four our puropose it was good enough.
Best
Christian
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