This is the Linux app named RGAAT whose latest release can be downloaded as RGAAT.tar.gz. It can be run online in the free hosting provider OnWorks for workstations.
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This program can assemble and/or annotate genome for new genome and known genome upgrade using sequence alignment file (SAM or BAM format), sequence variant file (VCF format or five coloum table (tab-delimited, including chromosome, position, id, reference allele and alternative allele)) or new genome sequence file (FASTA format) based on reference genome sequence file (FASTA format) and annotation file (TBL, GTF, GFF, GFF3 or BED format).
- sequence variation identification
- genome consensus sequence building
- genome modification
- genome comparison
- genome annotation
- building genome coordinate conversion between different genome assembly versions
This is an application that can also be fetched from https://sourceforge.net/projects/rgaat/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.