| Scaffhunter regroups several programs which principal aims are to work and visualize genetic mapping data. In addition to 2D visualization of linkage between markers, these tools can be used to order scaffolds without passing by the tedious step of genetic map construction and reconciliation between marker order in scaffold and marker order in the genetic map. |
hg clone https://toolshed.g2.bx.psu.edu/repos/gdroc/scaffhunter
| Name | Version | Type | |
|---|---|---|---|
| blast+ | 2.2.31 | package | |
| bowtie2 | 2.2.6 | package | |
| bwa | 0.7.7 | package | |
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| : Create a sub matrix of a matrix file | 0.1 | any | |
| : Assemble scaffolds in a chromosome | 0.1 | any | |
| : Correct GBS markers based on their order along scaffold or chromosome or other | 0.1 | any | |
| : Convert JoinMap pair-wise file to figure and create .dis and .don files for DARwin | 0.1 | any | |
| : Convert matrix to a dot-plot figure | 0.1 | any | |
| : Convert JoinMap pair-wise file to a tabulated matrix | 0.1 | any | |
| : Locate markers having uniq position on a reference | 0.1 | any | |
| : Order scaffold based on pseudo UPGMA method | 0.1 | any | |
| : Convert pair-wise file to a tabulated matrix | 0.1 | any | |
| : Perform local rearrangment between scaffold ordered based on the UPGMA | 0.1 | any | |