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Question: De novo assembly of a large insertion with a mapped-read seed.
1
gravatar for Pierre Lindenbaum
6.4 years ago by
Pierre Lindenbaum ♦ 134k
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum ♦ 134k wrote:

short story:

we are trying to identify the content of a large insertion localized at a known place in the human genome. Do you know an existing software that is able to start and extend a de-novo assembly from a read mapped to the REF sequence  ?

 

 

long story:

* my collaborators have sequenced the region of interest using IOn-torrent + mate-pair. As far as I can see, there are a lot of mismatches in the aligned reads.

* my BWA alignement  returns a poor depth in the region of interest (~ 2 )

* CGH shows that the insertion is a junction of a head-to-head duplication

 

 
structural denovo variation ngs assembly • 2.4k views
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modified 6.4 years ago • written 6.4 years ago by Pierre Lindenbaum ♦ 134k
1
gravatar for Pierre Lindenbaum
6.4 years ago by
Pierre Lindenbaum ♦ 134k
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum ♦ 134k wrote:

posting ‏@BaCh_mira 's answer on twitter here :
ADD COMMENT • link written 6.4 years ago by Pierre Lindenbaum ♦ 134k
0
gravatar for Devon Ryan
6.4 years ago by
Devon Ryan ♦ 98k
Freiburg, Germany
Devon Ryan ♦ 98k wrote:

Have you tried making a faux set of reads from the neighboring reference sequence and then seeing what trinity outputs when you try to assemble those along with the other reads? You could just blast the neighboring sequence against the resulting contigs to quickly narrow down which ones are candidates (assuming the results are worthwhile). Something like that might be worth a try at least.
ADD COMMENT • link written 6.4 years ago by Devon Ryan ♦ 98k

moving to an answer for the discussion. I tried to run vevlet with the reads mapped in the ROI and the unmapped reads: no contig of interest was created (= large number of short contigs)

ADD REPLY • link written 6.4 years ago by Pierre Lindenbaum ♦ 134k
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