Softwares to Assembly
Assemblet – Antigenic variation assembler.
Geneious – DNA alignment, assembly, and analysis software, but need to buy.
Mira – Sequence assembler and sequence mapping for whole genome shotgun and EST / RNASeq sequencing data. Can use Sanger, 454, Illumina and IonTorrent data. PacBio: PacBio: CCS and error corrected data usable, uncorrected not yet.
Wombac – Bacterial core genome SNPs for phylogenomic trees from NGS Reads and/or draft genomes.