What are the best reference based scaffolding tools for vertebrate genomes?

09 September 2019 1 4K Report

Hi all,

I am currently working on several newly assembled draft genomes ( which are at contig level). I would like to perform scaffolding using a reference based tool for my genomes. It would be highly appreciated if one can point out some good tools for the above mentioned purpose. Please note that I am currently running CSAR.

Cheers,

Anjana

Sureshkumar v.

Anjana Karawita

Check these sites.

https://github.com/fenderglass/Ragout

https://github.com/gtamazian/chromosomer

https://github.com/malonge/RaGOO

https://github.com/ablab-nthu/Multi-CSAR

Badges
Science topic

How can a reference point be fixed to an attachment point in Abaqus?

I am currently trying to copy an assembly feature, that is present in an old version of the model I am using, onto a new model. The feature is a reference point that is fixed to an attachment...

16 February 2021 8,872 2 View

Plasmid amplification in S2 cell?

When co-transfect S2 cell with selection vector (pCoHygro or pCoBlast ) to make a stable cell line, does the gene integrate into the genome or just like E.coli? How do the plasmids amplify within...

09 February 2021 5,423 1 View

Separated objects vs Non-Manifold Assembly?

I'm trying to do a simulation between the Maxilla and the Mandible I converted the Dicom file from the CT scan to a CAD module and module the articular discs via 3d software. I have two options...

08 February 2021 8,731 2 View

How to model Type 1 collagen structure for finite element analysis ?

I have started a project in which stress distribution in Type 1-collagen scaffold is to be modelled. I am thinking of using finite element analysis to model the structure and the loading...

07 February 2021 5,487 3 View

How do I apply continuity boundary condition at the edge using form assembly in comsol?

The continuity boundary condition is automatically created for a shared (common) surface boundary but I want to have it for an edge. Please help me out. In image 8 is the base of the cylinder and...

05 February 2021 3,459 2 View

Identical spectra for L- and D-peptides after they self-assemble?

Hi dear all, I need advice. I have two peptides with the same sequence but one consists of L-amino acids only and the other consists of D-amino acids only. when they self-assemble in aqueous...

03 February 2021 2,032 3 View

Could someone please suggest a suitable program for assembling plasmids containing repetitive sequences from short paired-end reads?

Hello! I'm trying to assemble some plasmid vectors that contain two repetitive regions (with around 500 and 250 bp) and it is being hard to get the complete sequence. If someone knows a better...

03 February 2021 6,379 3 View

Whether L version and D version peptidesshould have identical NMR, especially in the state of self-assembly?

Whether L version and D version peptides should have identical NMR, especially in the state of self-assembly have to have identical NMR? How to use HRMS to confirm L version or D version...

01 February 2021 6,756 4 View

How can i improve my DNA purity for whole genome sequence that has high 260/230 ratio ?

I am performing whole genome sequence for gram negative acinetobacter baumannii using two platforms illumina miswq and oxford nanopore. Thus i require a very high yield and high purity. I am using...

31 January 2021 355 2 View

Gibson PCR and reaction challenges, any tips?

Hi I am having issue's with Gibson assembly, seeing as I am new in the filed of cloning, expert feedback would be very much appreciated I am trying to clone two fragments (frag 1 [185bp, 145bp w/o...

29 January 2021 1,406 2 View