| These tools provide the main mapping-by-sequencing functionality of MiModD. Note that sequence reads have to be aligned to the corresponding reference genome before they can be analyzed. This can be done with any modern aligner of your choice or through the MiModD Read Alignment tool available from the separate repository mimodd_aln. Functional annotation of identified variants can be performed using SnpEff. MiModD-specific wrappers for SnpEff are available from the separate repository mimodd_snpeff though more general wrappers should be compatible, too. |
hg clone https://toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| takes a BAM file and generates a copy with the original header (if any) replaced or modified by that found in a template SAM file | 0.1.8_1 | 16.01 | |
| predicts deletions in one or more aligned paired-end read samples based on coverage of the reference genome and on insert sizes | 0.1.8_1 | 16.01 | |
| takes a SAM/BAM dataset and generates a coordinate/name-sorted copy | 0.1.8_1 | 16.01 | |
| in a human-friendly format that simplifies data exploration | 0.1.8_1 | 16.01 | |
| from a BCF file | 0.1.8_1 | 16.01 | |
| converts sequence data into different formats | 0.1.8_1 | 16.01 | |
| maps phenotypically selected variants by multi-variant linkage analysis | 0.1.8_1 | 16.01 | |
| writes run metadata in SAM format for attaching it to sequenced reads data | 0.1.8_1 | 16.01 | |
| extracts lines from a vcf variant file based on field-specific filters | 0.1.8_1 | 16.01 | |
| calculates coverage statistics for a BCF file as generated by the MiModd Variant Calling tool | 0.1.8_1 | 16.01 | |
| provides summary reports for supported sequence data formats. | 0.1.8_1 | 16.01 | |
| generates a BCF file of position-specific variant likelihoods and coverage information based on a reference sequence and reads aligned against it | 0.1.8_1 | 16.01 | |
| from a VCF file | 0.1.8_1 | 16.01 | |