| Scaffremodler can be used to improve scaffold assemblies or to detect large structural variations between a reference sequence and a re-sequenced genome. |
hg clone https://toolshed.g2.bx.psu.edu/repos/gdroc/scaffremodler
| Name | Version | Type | |
|---|---|---|---|
| bowtie2 | 2.2.6 | package | |
| bwa | 0.7.7 | package | |
| picard | 1.136 | package | |
| samtools | 1.2 | package | |
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| : Filter paired read mapping uniquely that pass mapping quality threshold | 0.1 | any | |
| : Parse mapped reads based on their discordance type | 0.1 | any | |
| : Join scaffolds unsing a tabulated file | 0.1 | any | |
| : Create configuration file and files needed to draw circos | 0.1 | any | |
| : Draw circos figure | 0.1 | any | |
| : Map read onto a reference fasta file | 0.1 | any | |
| : Create a file grouping scaffold name that should be joined together | 0.1 | any | |
| : Identify discordant zones | 0.1 | any | |
| : Look for possible scaffold fusions and junction using Scaffremodler workflow and conf4circos outputs | 0.1 | any | |
| : Try to identify pattern of structural variation | 0.1 | any | |
| : Calculate statistics on insert size, and coverage | 0.1 | any | |
| : Merge scaffolds using a tabulated file | 0.1 | any | |
| : Generate circos to verifies sequence fusions and junctions | 0.1 | any | |
| : Remove redundancy in mapped reads | 0.1 | any | |
| : Replace specified DNA regions (in the provided table file) by X | 0.1 | any | |
| : Re-estimate N in multifasta (N restimated are converted to S) | 0.1 | any | |
| : Create configuration file and chromosome tab file for Scaffremodler | 0.1 | any | |
| : Split fasta sequence on X and rename sequence based on length | 0.1 | any | |