A sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular format that can be used for quality control steps. PRINSEQ is available as both standalone and web-based version.
Tool to automatically detect and efficiently remove tag sequences (e.g. WTA or MID tags) from metagenomic datasets. TagCleaner is available as both standalone and web-based version.
Tool to automatically detect and efficiently remove any type of known sequence contamination from metagenomic datasets. The tool uses a modified version of the BWA-SW aligner and can be applied to longer-read datasets (150+bp read length). DeconSeq is available as both standalone and web-based version.
Tool to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic datasets. The tool was designed to process longer-read datasets (150+bp read length), but works on 100+bp reads too. riboPicker is available as both standalone and web-based version.
Metagenome annotation services across several platforms of technology, which include CGI scripting and web services (RTMg.web), the new Android cell phone operating system (RTMg.mob), and all OpenSocial-based social network sites (RTMg.os)
SEED database tools
The SEED database of microbial genomes is used in many projects. We work with our colleagues at Argonne National Laboratory to develop the SEED and tools that access and use it.
SUPER-FOCUS: An agile homology-based approach using a reduced SEED database to report the subsystems present in metagenomic samples and profile their abundances.
CCOM: This web-based tool is used to reconstruct the uncultured genome from environmental samples.
Tools for genomic data
Software to order contigs generated by draft sequencing along a reference sequence. Gaps are filled with N’s and small overlaps are aligned with Muscle and the consensus created with IUPAC codes. Scaffold_builder can help in the assembly and annotation of genomes by revealing what is missing and allowing targeted sequencing to close those gaps.
Tools for phage data
We are developing the PHage ANnotation TOols and MEthods (PhAnToME) site in collaboration with researchers in Arizona, Florida, and Virginia. Most of those tools are being released through that website.
PHAge Classification Tool Set or PHACTS is a web based program that is used to calculate whether a phage is lytic or lysogenic.
An interactive app for searching genomes at the SEED.
Documentation for a tool which handles custom capture, save, and viewing of images taken with an Allied Vision Technologies camera.
Source code is available on github at: https://github.com/linsalrob/cameraGUI
Tools for coral reef biology
Coral Reef Photography
New software that allows you to analyze images from coral reefs and identify movement from the background noise.
The SEED database of microbial genomes is one that we use all the time. We work with our colleagues at Argonne National Laboratory to develop the SEED and tools that access and use it. Here are some of the tools that we have developed around the SEED. After the read more you can learn all about how we access the SEED…