Arpita Ghosh

6 Questions 14 Answers 0 Followers

Questions related from Arpita Ghosh

How do I circularize a plant mitochondrial genome using a de novo based approach?

I have NextSeq and MiSeq PE data which i have assembled using Newbler v2.6, CLC and velvet. The best assembly was obtained from Newbler. I have extracted the scaffolds related to mitochondrial...

12 December 2014 9,794 5 View

How do you identify transposons in leishmania, specially SIDERs?

Can any one suggest any tool or any bioinfomatics approach to do so?

12 December 2014 2,126 2 View

I want to merge two contigs together make one scaffold.Can anyone suggest some tools?

I have tried SSPACE were the contigs are extending but not merging in one to form a scaffold. For assembly i have used gsASSEMBLER. Kindly suggest.

09 September 2014 924 1 View

How to use SSPACE for scaffolding ?

I have an hybrid contigs of 454 + Illumina + SOLiD which is around 850 Mb. Now I want to create scaffolds using SSPACE with 20kb (3 libraries) of 454 paired end reads which have been converted...

08 August 2012 6,510 4 View

Hybrid assembly of complex genome

I have an hybrid data of 454 + Illumina + SOLiD which i have assembled into 157439 contigs covering around 1.3 GB genome. Now I want to create scaffolds using 20kb (3 libraries) 454 paired end...

07 July 2012 6,213 6 View

Hybrid Assembly of Complex Genomes

I am trying to assemble hybrid reads using PE and BAC reads. I have shredded the sequences 1Kb with 800bp overlap and I am assembling with Newbler. I am giving input of 1 GB but getting output of...

07 July 2012 6,151 7 View