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Repository scaffhunter
Name: scaffhunter
Owner: gdroc
Synopsis: Scaffhunter
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.  
Type: unrestricted
Revision: 2:ec31e4883c99
This revision can be installed: True
Times cloned / installed: 224
Dependencies of this repository

Repository package_bwa_0_7_7 revision def70e393020 owned by iuc
Repository package_blast_plus_2_2_31 revision 921d2963a177 owned by iuc
Repository package_bowtie_2_2_6 revision 0d9cd7487cc9 owned by iuc

Name Version Type
blast+ 2.2.31 package
bowtie2 2.2.6 package
bwa 0.7.7 package

Contents of this repository

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

Categories
Assembly - Tools for working with assemblies