UMD students, let me know if you are interested in participating in one
of the following two projects:
AMOS
enhancements
AMOS
documentation projectSoftware
- AMOS
- Modular,
open-source framework for developing assembly algorithms.
Among
the programs developed within the AMOS framework are:
- AMOScmp
- comparative sequence assembler. AMOScmp was used in a study
that identified the presence of the bacterial endosymbiont Wolbachia within
several fruit fly
genomes (see paper).
- Minimus
- streamlined assembly program developed specifically for small
assembly tasks (single genes, BACs, viral genomes). Minimus
is
being used to assemble a collection of strains of the flu virus (see project
website).
- Bambus
-
the first publicly-available standalone scaffolding program.
- Figaro - "blind" vector trimming software (coming soon)
- SOMA - scaffolder for optical maps (coming soon)
- Bacterial genome annotation pipeline (in progress)
- 454-Sanger hybrid assembler (in progress)
- Metagenomic analysis pipeline (in progress)
Databases
- Conserved genomic elements in bacteria (in progress)
- Antibiotic resistance factors in bacteria (in progress)
