Tools for metagenomic and metatranscriptomic data
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PRINSEQ
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.
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TagCleaner
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.
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DeconSeq
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.
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riboPicker
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.
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Xipe-Totec
A statistical tool written by Beltran Rodriguez in Forest Rohwer's lab. We used it to analyze the first pyrosequencing-based metagenomes (from the Soudan Mine in Minnesota) and the original Sargasso Samples from Venter. You can download the source code of Xipe-totec, or use the online version of the tool.
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RTMg
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)
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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.
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Tools for genomic data
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Scaffold_builder
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.
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Tools for phage data
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PhAnToMe
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.
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PHACTS
PHAge Classification Tool Set or PHACTS is a web based program that is used to calculate whether a phage is lytic or lysogenic.
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Phage Proteomic Tree
A phylogentic classic that is so good its in text books!
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The Phage SEED
Database for annotating and comparing phage genomes.
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The Phage Biobike
A graphical programming language for non-computer scientists to analyze biological data.
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Phage Eco-Locator
Tool to identify phages in metagenomes.
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PhiSpy
A novel algorithm for finding prophages in microbial genomes that combines similarity-based and composition-based strategies.
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Tools for mobile devices
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Software
