1. Reference sequences loaded and transformed into contigs, each contig
containing exactly one read.
2. Sequence of each contig is cut into overlapping pieces (called rails).
Length of rails: 2* longest read to map. Overlap: length of longest read to
map. Rails are inserted as pseudo reads into contigs.
3. SKIM (fast overlap search) of reads to map against rails.
4. Smith-Waterman (SW) check of potential mapping sites, only best match of a
read against rail is kept.
5. Multiple stage mapping:
5a Mapping of SW where the ends of the overlap are “clean”, i.e., no mismatch
in the last 28bp left and right of the overlap.
5b Repeat 5a for 24, 20, 16, 12, 8, 4 bp
5c Map reads where SW overlap has one mismatch
5d Map reads where SW has one indel
5e Map reads where SW has two mismatches
5f Map reads with one mismatch, one indel
5g Map reads with two indels
5h Map reads with 3 difference (don’t bother about mismatch or indel).
5i Repeat 5h with 4, 5, 6, … n differences, until maximum allowed number of
differences reached.
6. (Optional, but do the following exactly once:) If bootstrapping is used, use
the now available alignment to calculate a consensus. This consensus is used to
recalculate rail sequences which then contain the current best guess of the
mapped sequence. Remove all mapped reads, go back to 5a
7. Remove rails from contigs.
8. Search for discrepancies between original reference sequences and mapped
sequence, mark them with tags for SNPs.
9. Write results.
10. Done.
On 22 Jun 2016, at 8:02 , Vasileios Panagiotis Lenis [vpl] <vpl@xxxxxxxxxx>
wrote:
Hello Bastien,
Thank you very much for your super fast answer. :)
I would like to put a small description of the steps that MIRA follows for
the ref based assembly (like mapping the reads on the reference with xxx,
etc.) and if its possible to have a figure with the workflow.
Thank you very much,
Vasilis.
On 22 Jun 2016, at 12:51, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
So what exactly do you need to know? :-)
B.
On 22 Jun 2016, at 7:41 , Vasileios Panagiotis Lenis [vpl] <vpl@xxxxxxxxxx>
wrote:
Hello all,
I芒鈧劉m really sorry for bothering you with such a naive question, but since
I am trying to write my thesis and I have used MIRA for a reference-guided
assembly, I am trying to find more information about the workflow that MIRA
follows for this type of assembly. I have found a great explanation about
the de novo assembly with a fantastic workflow figure but unfortunately I
haven芒鈧劉t found something similar for the reference-guided.
I know that your time is limited in order to answer in serious questions
about technical problems but I would really appreciate it if you could
provide me with this kind of information.
Thank you very much in advance,
Vasilis.
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Study at Aberystwyth 鈥� Wales鈥� First University
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