Hi Everyone –

This is a note for COLSA users of the premise cluster regarding some recent software additions.

The following software is now available on the cluster, with more coming soon.  This list is also available at http://premise.sr.unh.edu/#modules.  As a reminder, the premise cluster will be offline tomorrow starting at 6:45am for maintenance. Thanks –

• ABySS 2.0.2 -- Paired-end short read sequence assembler. website
• Augustus 3.2.2 -- Gene prediction in eukaryotic genomic sequences. website
• BamTools 2.4.0 -- Toolkit for working with BAM (Binary Alignment Map) data. website
• BedTools 2.26.0 -- Toolkit for performing a variety of genomics analysis tasks. website
• BFC r181 -- Illumina read error correction website
• BLAST Suite 2.5.0 -- Nucleotide/Protein alignment against nucleotide/protein references. website
• Bowtie 1.1.2 -- Nucleotide (<50 bp) alignment against nucleotide references. website
• Bowtie 2 2.2.9 -- Nucleotide (>50 bp) alignment against nucleotide references. website
• BUSCO 1.22 -- Assessment of genome assemblies, gene sets, and transcriptome completeness. website
• BWA 0.7.15 -- Nucleotide alignment against nucleotide references. website
• Canu 1.4 -- High-noise, single-molecule (PacBio RS II / Oxford Nanopore MinION) assembler. website
• CD-HIT 4.6 -- Nucleotide and protein cluster creation and comparison. website
• dammit 0.3.2 -- De novo transcriptome annotator. website
• ExaBayes 1.5 -- Bayesian inference of phylogeny for computer clusters. website
• Exonerate 2.2.0 -- Nucleotide and protein alignment against nucleotide and protein references. website
• FASTX-Toolkit 0.0.14 -- Collection of tools for short-read FASTA/FASTQ files. website
• HMMER 3.1b2 -- Homolog search and sequence alignment using hidden Markov models. website
• Infernal 1.1.2 -- Inference of RNA alignments. website
• Jellyfish 2.2.6 -- K-mer counting and analysis. website
• Kallisto 0.43.0 -- Quantify abundances of transcripts from RNA-Seq data. website
• MAFFT 7.305b -- Nucleotide/Protein multiple sequence alignment. website
• Maker 2.31.9 -- Annotation of prokaryotic/eukaryotic genomes. website
• MrBayes 3.2.6 -- Bayesian inference of phylogeny. website
• MUSCLE 3.8.1551 -- Nucleotide/Protein multiple sequence alignment. website
• PALADIN 1.3.1 -- Nucleotide alignment and UniProt reporting against annotated nucleotide/transcriptome/protein references. website
• PEAR 0.9.10 -- Paired-end read merger. website
• Perl 5.24.0 -- Perl programming language. website
• PRANK 140603 -- Probabilistic multiple sequence alignment for closely related sequences. website
• Prodigal 2.6.2 -- Bacterial/Archaeal gene finding. website
• Prokka 1.11_1 -- Annotation of prokaryotic genomes. website
• Python 2 2.7.13 -- Python programming language. website
• Python 3 3.6.0 -- Python programming language. website
• QUAST 4.4.1 -- Quality assessment of genome assemblies. website
• QuorUM 1.0.0 -- Illumina read error correction. website
• Plink 1.07 -- Whole genome data analysis toolset. website
• R 3.3.2 -- R programing language. website
• RAxML 8.2.9 -- Maximum-Likelihood inference of phylogeny. website
• Rcorrector 1.0.2 -- Illumina RNA-seq error correction. website
• Repeatmasker 4.0.5 -- DNA repeat and low complexity detection. website
• Salmon 0.7.2 -- Quantify abundances of transcripts from RNA-Seq data. website
• Skewer 0.2.2 -- Adapter trimmer for paired-end reads. website
• SNAP 2013-11-29 -- Semi-HMM-based gene prediction tool. website
• SPAdes 3.9.0 -- Small genome assembly toolkit. website
• Transdecoder 3.0.1 -- Identify candidate coding regions within transcripts. website
• Trimmomatic 0.36 -- Illumina read trimming tool. website
• Trinity 2.3.2 -- Illumina RNA-seq read sequence assembler. website

Toni Westbrook

Computational Scientist

Research Computing Center, College of Life Sciences and Agriculture

University of New Hampshire

Offices: 219 Morse Hall, 436 Gregg Hall