Software packages developed in the Pop lab

The members of the Pop lab have a strong commitment to releasing usable software tools to the community. This software is provided open-source with the intention of allowing researchers to re-use and extend our ideas. We distribute our software both through our website and github respository, as well as through the MarBL (Maryland Bioinformatics Labs) repository, site maintained in the collaboration with the Phillippy, Salzberg, and Schatz laboratories.

IMPORTANT DISCLAIMER: The software listed below represent packages developed over many years, most of which are no longer under active development. We do our best to make the old source-code available but unmaintained software is provided as-is and we cannot provide any other assistance. We can only provide personal help for software packages under active development.

Software under active development

MetagenomeScope – Software for visualizing (meta)genome assembly graphs.
MetaCarvel – Scaffolder for metagenomic data. Also see publication: Ghurye, J., Treangen, T., Fedarko, M. et al. Genome Biol (2019) 20: 174. https://doi.org/10.1186/s13059-019-1791-3
ATLAS – Outlier detection in BLAST results for taxonomic identification. Also see publication: Shah N, Meisel JS and Pop M (2019) Embracing Ambiguity in the Taxonomic Classification of Microbiome Sequencing Data. Front. Genet. 10:1022. https://doi.org/10.3389/fgene.2019.01022
Metacompass – Reference-guided assembly for metagenomic data.
VALET – De novo ssembly validation suite for metagenomic data. Also see: Nathan D Olson, Todd J Treangen, Christopher M Hill, Victoria Cepeda-Espinoza, Jay Ghurye, Sergey Koren, Mihai Pop, Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes, Briefings in Bioinformatics, Volume 20, Issue 4, July 2019, Pages 1140–1150, https://doi.org/10.1093/bib/bbx098

Historical software by category

Metagenomics

  • metAMOS – assembly and analysis pipeline for metagenomic data.
  • MaryGold – software for graph-based analysis of genomic variation within metagenomic assemblies.
  • Bambus 2 – scaffolder for metagenomic data. Explicitly accounts for and detects genomic variants.
  • MetagenomeSeq – statistical package for differential abundance in metagenomic case/control studies. Relies on a linear model framework and includes a zero-inflated component to handle sparsity. Maintained by Corrada Bravo lab – http://www.hcbravo.org/
  • Metastats – statistical package for differential abundance in metagenomic case/control studies based on non-parametric t-test.

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

Short-read assembly/alignment

  • Bowtie – fast aligner based on Burrows-Wheeler transform. Maintained by Langmead labhttp://www.langmead-lab.org.
  • Minimus-SR – Version of minimus that works with short reads.

Databases

  • ARDB – Antibiotic resistance factors in bacteria
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