Software

Categories: pipelines, bioinformatics tools, and statistics and visualization tools.

Pipelines

Sunbeam

Sunbeam is a modular, extensible pipeline for the analysis of metagenomic sequencing data.
Sunbeam Project on GitHub
Sunbeam Documentation
Current developers: Charlie Bushman, Kyle Bittinger (PI)
Language: Python, Bash
License: GPL2+
Citation: Clarke EL, Taylor LJ, Zhao C, Connell A, Lee JJ, Fett B, Bushman FD, Bittinger K. Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments. Microbiome. 2019 Mar 22;7(1):46. PMID: 30902113; PMCID: PMC6429786.

INSPIIRED

A software suite designed to study viral integration sites and the longitudinal outcomes of gene therapy patients.
INSPIIRED Project on GitHub
Current developers: John Everett, Rick Bushman (PI)
Language: R
License: GPL3
Citation: Berry CC, Nobles C, Six E, Wu Y, Malani N, Sherman E, Dryga A, Everett JK, Male F, Bailey A, Bittinger K, Drake MJ, Caccavelli L, Bates P, Hacein-Bey-Abina S, Cavazzana M, Bushman FD. INSPIIRED: Quantification and Visualization Tools for Analyzing Integration Site Distributions. Mol Ther Methods Clin Dev. 2016 Dec 18;4:17-26. PMID: 28344988; PMCID: PMC5363318.

Bioinformatics

Unassigner

Species-level assignment for 16S rRNA marker gene sequences, but with a twist.
Unassigner Project on GitHub
Current developers: Ceylan Tanes, Kyle Bittinger (PI)
Language: Python
License: GPL2+

GNUVID

Gene Novelty Unit-based Virus IDentification for SARS-CoV-2.
GNUVID Project on GitHub
Current developers: Ahmed Moustafa (PI), Paul Planet (PI)
Language: Python
License: GPL3
Citation: Moustafa AM, Planet PJ. Emerging SARS-CoV-2 Diversity Revealed by Rapid Whole-Genome Sequence Typing. Genome Biol Evol. 2021 Sep 1;13(9):evab197. PMID: 34432021; PMCID: PMC8449825.

WhatsGNU

What's Gene Novelty Unit: A Tool For Identifying Proteomic Novelty.
WhatsGNU Project on GitHub
Current developers: Ahmed Moustafa (PI), Paul Planet (PI)
Language: Python
License: GPL3
Citation: Moustafa AM, Planet PJ. WhatsGNU: a tool for identifying proteomic novelty. Genome Biol. 2020 Mar 5;21(1):58. PMID: 32138767; PMCID: PMC7059281.

BROCC

Consensus-based taxonomic assignment using BLAST results.
BROCC Project on GitHub
Current developer: Kyle Bittinger (PI)
Language: Python
License: GPL3
Citation: Dollive S, Peterfreund GL, Sherrill-Mix S, Bittinger K, Sinha R, Hoffmann C, Nabel CS, Hill DA, Artis D, Bachman MA, Custers-Allen R, Grunberg S, Wu GD, Lewis JD, Bushman FD. A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples. Genome Biol. 2012 Jul 3;13(7):R60. PMID: 22759449; PMCID: PMC4053730.

DNAbc

Identify DNA barcodes in FASTQ data files and write demultiplexed data.
DNAbc Project on GitHub
Current developer: Kyle Bittinger (PI)
Language: Python
License: GPL2

primertrim

Detect short primer sequences in FASTQ reads and trim the reads accordingly.
primertrim Project on GitHub
Current developer: Charlie Bushman, Kyle Bittinger (PI)
Language: Python
License: GPL2

Stackebrandt Curves

Compare whole-genome similarity to 16S rRNA gene similarity.
Stackebrandt Curves Project on GitHub
Current developer: Kyle Bittinger (PI)
Language: Python
License: GPL3

okfasta

Utilities for FASTA-format sequence files, implemented in pure Python.
okfasta Project on GitHub
Current developer: Kyle Bittinger
Language: Python
License: MIT

Statistics and Visualization

mirix

Model the susceptibility of a bacterial community to antibiotics.
mirix Project on GitHub
Current developers: Ceylan Tanes, Kyle Bittinger (PI)
Language: R
License: GPL3
Citation: Tu V, Ren Y, Tanes C, Mukhopadhyay S, Daniel SG, Li H, Bittinger K. A quantitative approach to measure and predict microbiome response to antibiotics. bioRxiv 2023.01.27.525904.

ZIBR

Zero-inflated beta random effect model for microbiome data.
ZIBR Project on GitHub
Current developers: Eric Chen, Hongzhe Li (PI)
Language: R
License: GPL2
Citation: Chen EZ, Li H. A two-part mixed-effects model for analyzing longitudinal microbiome compositional data. Bioinformatics. 2016 Sep 1;32(17):2611-7. Epub 2016 May 14. PMID: 27187200; PMCID: PMC5860434.

ZIR

Zero-Inflated (Wilcoxon and Kruskal–Wallis) Rank Test.
ZIR Project on GitHub
Current developers: Eric Chen, Hongzhe Li (PI)
Language: R
License: GPL2
Citation: Wanjie Wang, Eric Z. Chen, Hongzhe Li. Truncated Rank-Based Tests for Two-Part Models with Excessive Zeros and Applications to Microbiome Data.

microflowseq

Analyze microbiome data from bacterial cell sorting (mFLOW-Seq) experiments.
microflowseq Project on GitHub
Current developers: Ceylan Tanes, Charlie Bushman, Kyle Bittinger (PI)
Language: R
License: MIT
Citation: Conrey PE, Denu L, O'Boyle KC, Rozich I, Green J, Maslanka J, Lubin JB, Duranova T, Haltzman BL, Gianchetti L, Oldridge DA, De Luna N, Vella LA, Allman D, Spergel JM, Tanes C, Bittinger K, Henrickson SE, Silverman MA. IgA deficiency destabilizes homeostasis toward intestinal microbes and increases systemic immune dysregulation. Sci Immunol. 2023 May 26;8(83):eade2335. Epub 2023 May 26. PMID: 37235682.

polyafit

Identify enriched features in paired microbiome samples.
polyafit Project on GitHub
Current developer: Kyle Bittinger (PI)
Language: R
License: GPL2+
Citation: Charlson ES, Bittinger K, Chen J, Diamond JM, Li H, Collman RG, Bushman FD. Assessing bacterial populations in the lung by replicate analysis of samples from the upper and lower respiratory tracts. PLoS One. 2012;7(9):e42786. Epub 2012 Sep 6. PMID: 22970118; PMCID: PMC3435383.

usedist

Efficiently create, modify, and extract information from distance matrices.
usedist Project on GitHub
Current developer: Kyle Bittinger
Language: R
License: GPL3

adonisplus

A data-pipeline-friendly interface to the PERMANOVA or Adonis test.
adonisplus Project on GitHub
Current developer: Kyle Bittinger
Language: R
License: GPL3

abdiv

Reference implementation for measures of alpha and beta diversity.
abdiv Project on GitHub
Current developer: Kyle Bittinger
Language: R
License: MIT

pheatbuilder

A data-pipeline-friendly interface to build heatmap charts.
pheatbuilder Project on GitHub
Current developer: Kyle Bittinger
Language: R
License: GPL3

taxafmt

Format and parse taxonomic assignments, especially for microbiome data.
taxafmt Project on GitHub
Current developer: Kyle Bittinger
Language: R
License: MIT