Shameless plug: MIRA3 at SourceForge with the the corresponding Wiki where you can find the full manual online. It is one self-contained binary, ready to run if you download the binary package.
Input formats can be any of the usual suspects (FASTA, FASTQ, PHD, EXP), giving ancillary data is also possible (NCBI TRACEINFO XML, EXP, tab delimited files).
You might be interested in using the feature where you can assign strain data to your reads and have the assembler mark SNPs and other differences when assembling all reads together. This works both for mapping as well as for de-novo assemblies. See some examples here.
You can also tell the assembler which sequencing technologiy your (in this case simulated) sequences are and see how it influences assembly and SNP calling (e.g., indels will not be called SNPs in 454 sequences by default, but in Sanger and Illumina sequences they will).
On a last note: as you have no qualities, you will need to tell the assembler about it. See here for information on how to do that.
9.2 years ago by
Bach • 550