MicrobiomeUtilities - Browse /SEQSETS_CSLAYER

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Name	Modified	Size	InfoDownloads / Week
Parent folder
HMP_454_MOCK_EVEN.tgz	2010-12-11	28.5 MB	0
HMP_Sanger_MOCK_EVEN.tgz	2010-12-11	5.8 MB	0
HMP_MOCK_16SreferenceSeqs.tgz	2010-12-11	38.2 kB	0
HMP_454_MOCK_WGS.tgz	2010-12-11	427.6 kB	0
HMP_454_MOCK_STAG.tgz	2010-12-11	17.4 MB	0
HMP_454_MOCK_PCR_CONDITIONS_SEQS.tgz	2010-12-10	11.9 MB	0
Totals: 6 Items		64.1 MB	0

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Recommended Projects

DNA Clust
A tool for clustering large number of short similar DNA sequences. This program is originally designed for clustering targeted 16S rRNA pyrosequencing reads.
riboPicker
A bioinformatics tool to identify and remove rRNA sequences from metagenomic and metatranscriptomic datasets. The rRNA-like sequences are classified by domain, subunit. and bacterial phyla. Coverage plots for the top hits are provided as well.
BADASS
BADASS is a software with a user-friendly graphical interface applied to the search and analysis of bacteriocin diversity in whole-metagenome shotgun sequencing data. The search for bacteriocin sequences is performed with tools such as BLAST or DIAMOND using the BAGEL4 database as a reference. The putative bacteriocin sequences identified are used to determine the abundance and richness of the three classes described so far. Abundance is calculated by comparing the reads identified as bacteriocins to the reads identified as 16S rRNA gene using SILVA database as a reference. The user is able to change the main parameters of the analysis in the graphical interface.
RDP Classifier
The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments for bacterial and archaeal 16S rRNA sequences, fungal LSU and fungal ITS sequences, with confidence estimates for each assignment. More information and tutorials on how to install, use and retrain RDP Clasifier can be found on at https://github.com/rdpstaff/classifier and John Quensen's blog (https://john-quensen.com/). Citation: 1. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007 Aug;73(16):5261-7. 2. Wang Q, Cole JR. Updated RDP taxonomy and RDP Classifier for more accurate taxonomic classification. Microbiol Resour Announc. 2024 Apr 11;13(4):e0106323.
BarraCUDA Fast Short Read Aligner
Barracuda is a high-speed sequence aligner based on Sanger's BWA and utilizes the latest Nvidia CUDA architecture for accelerating alignments of sequence reads generated by next-generation sequencers.

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