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SPAdes

SPAdes  (St. Petersburg genome assembler) is an assembly toolkit with a variety of assembly pipelines.

Trinotate

Trinotate is a transcriptome annotation suite designed for use with de novo assembled transcriptomes from model or non model organisms.

RNAmmer

RNAmmer is software for predicting ribosomal RNA in full gene sequences.

To use this program at MSI, please send a a request to help@msi.umn.edu and ask to be added to the RNAmmer group. The use of RNAmmer at MSI is limited to academic researchers.

TMHMM

TMHMM is software for the prediction of transmembrane helices in proteins.

 

To use this program at MSI, please send a a request to help@msi.umn.edu and ask to be added to the TMHMM group. The use of TMHMM at MSI is limited to academic researchers.

BRAKER1

BRAKER1 is software for unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS.

SignalP4

SignalP4 is software for predicting the presence and location of signal peptide cleavage sites in amino acid sequences in different organisms.

 
To use this program at MSI, please send a a request to help@msi.umn.edu and ask to be added to the SignalP4 group. The use of SignalP4 at MSI is limited to academic researchers.

TransDecoder

TransDecoder is software for identifying candidate coding regions within transcript sequences, including those from de novo RNA-Seq transcript assembly via Trinity, or from RNA-Seq alignments to the genome using Tophat and Cufflinks.

GeneMark-ET

GeneMark is the name of a set of gene prediction programs developed at the Georgia Institure of Technology. Genemark-ET is a member of this set of software for semi-supervised analysis of novel genomes.

To use this program at MSI, please send a a request to help@msi.umn.edu and ask to be added to the GeneMark group. The use of GeneMark at MSI is limited to academic researchers.

 

 

JAGS

JAGS (Just Another Gibbs Sampler) is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.

 

 

 

 

PBSuite aka PBJelly

PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles. PBJelly fills or reduces as many captured gaps as possible to produce upgraded draft genomes. Each step in PBJelly’s workflow can be run on a cluster, thus parallelizing the gap filling process for rapid turn around, even for very large eukaryotic genomes.

http://sourceforge.net/p/pb-jelly/wiki/Home/

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