-
v1.3 Release: magatt-1.3
NEW: ISBPs anchoring on target genome is now included in the pipeline ISBPs are provided as a BED file. Their sequences are extracted from the source genome with `bedtools getfasta` and then mapped on the target genome using `bwa mem`
-
v1.2
Major improvements: - GMAP rescue on whole genome now run at the end of each chromosome batch. Major boost in execution time of the whole pipeline - GMAP index: the indexing of the target with gmap_build has been removed. the index must be specified in the config.yaml file with `targetGmapIndex` (for -d option of gmapl) and `targetGmapIndexPath` (for -D option of gmapl) Bugs: some bugs were corrected - reformatGmapWGGFF.py : bad initialisation of chromosomeMap dictionary - renameGffID.py: bad initialisation of chromosomeMap dictionary
-
v1.1
Stable version 1.1: New single-isoform feature
-
v1.0
First V1.0 of pipeline
-
v0.3
New version with Whole genome Gmap results integrated into the final GFF. CDS are also validated using fastavalidcds from exonerate