Software packages developed in the Pop lab

UMD students, let me know if you are interested in participating in one of the following two projects:
AMOS enhancements
AMOS documentation project

Assembly

• 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). Also, an extension (Minimus-SR) was written to handle short-read sequencing data.
• Bambus - the first publicly-available standalone scaffolding program.
• Figaro - "blind" vector trimming software
• SOMA - scaffolder for optical maps
• DYIG (do it yourself genomics) Bacterial genome annotation pipeline
• 454-Sanger hybrid assembler

Metagenomics

• Metastats - statistical comparison of metagenomic libraries
• Metagenomic analysis pipeline

Short-read assembly/alignment

Also see Short Read Assembly page.

• Bowtie - fast aligner based on Burrows-Wheeler transform
• Minimus-SR - Version of minimus that works with short reads.

Annotation

• DYIG (do it yourself genomics) Bacterial genome annotation pipeline

Databases

• ARDB - Antibiotic resistance factors in bacteria
• Conserved genomic elements in bacteria (in progress)

Last modified March 9, 2009