![]() The steps involved in the alignment lead to more gene chimeras and strange coverage patterns within each contig that may be expected from a 'correct' approach. The reason I am looking into mira3 now is that, it appears that the de novo alignment algorithm is not totally appropriate for RNA-seq projects. It is, however, highly suggested to use the software on a 64 bit system with plenty of ram (8 gigs and up).Īll this comes at the price of some flexibility and some transparency, I guess. This we have done repeatedly and new comers in the lab get quickly to their results without too much of a chock. ![]() sff or fasta/fasta.qual data, trim sequences according to different criteria, do a de novo assembly, save consensus sequences from the contigs, do a reference assembly (possibly with only a subset of sequences), look for SNPs, export SNP tables and ACE assembly files. For example, using menus, it is easy to import. I would say that the main strength of CLC is it's easiness of use, mainly for non-computer-oriented biologists, or even for non-hardcore-linux users. We have mostly used the software to toy with RNA-seq 454 data in non-model species, so our expertise is with de-novo assembly of expressed sequences, namely cDNA from RNA containing poly-A tails. Nothing that you couldn't find in the open source world, but well put together. ![]() The software IS really a well integrated resources with a lot of small functionalities. We have been using CLC Genomic Workbench for the last year with great results. I work in a lab mainly into evolution and genomics in fishes. I am presently going the opposite way from what you do, coming from CLC, I am exploring (anew) the possibilities of open software (mainly mira3 now) for 454 assembly.
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