Hi Everyone –

Two COLSA related Premise updates:

1. For anyone needing to create an isolated environment for custom pipelines requiring older versions of software than currently installed, the Anaconda installation on Premise will allow you to easily maintain your own individual environments.  If you are interested in this functionality and are new to Anaconda, please shoot me an email and we can setup a time to meet.
2. A new batch of software has been installed – the new full list is as follows:

·  linuxbrew/colsa -- A collection of the following bioinformatics software:

• ABySS 2.0.2 -- Paired-end short read sequence assembler. website
• ARAGORN 1.2.36 -- Detection of tRNA and tmRNA in nucleotide sequences. 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
• Barrnap 0.7 -- Rapid ribosomal RNA predictor. website
• BayeScan 2.0 -- Detecting natural selection from population-based genetic data. website
• BedTools 2.26.0 -- Toolkit for performing a variety of genomics analysis tasks. website
• BFC r181 -- Illumina read error correction website
• BLASR 1.3.1 -- PacBio nucleotide alignment against nucleotide references. 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 2.0.1 -- 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
• E-MEM 1.0.0 -- Compute MEMs (maximal exact matches) between large genomes. website
• EMBOSS 6.6.0.0 -- Toolkit containing multiple applications for molecular biology analysis. 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
• FastQC 0.11.5 -- Quality control reporting tool for sequence data. website
• FASTX-Toolkit 0.0.14 -- Collection of tools for short-read FASTA/FASTQ files. website
• GATK 3.6 -- Toolkit for variant discovery and genotyping. 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
• MinCED 0.2.0 -- Find CRISPRs in shotgun DNA sequences or full genomes. website
• MCL 14-137 -- Unsupervised cluster algorithm for graphs (Markov Cluster Algorithm). website
• MrBayes 3.2.6 -- Bayesian inference of phylogeny. website
• MUSCLE 3.8.1551 -- Nucleotide/Protein multiple sequence alignment. website
• PALADIN 1.3.2 -- Nucleotide alignment and UniProt reporting against annotated nucleotide/transcriptome/protein references. website
• PALADIN-plugins 1.0.0 -- Pipeline for PALADIN related analysis. website
• PEAR 0.9.10 -- Illumina Paired-end read merger. website
• Perl 5.24.0 -- Perl programming language. website
• Plink 1.07 -- Whole genome data analysis toolset. website
• PRANK 140603 -- Probabilistic multiple sequence alignment for closely related sequences. website
• PRODIGAL 2.6.2 -- Microbial gene finder. 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
• 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 4.0.7 -- DNA repeat and low complexity detection. website
• Roary 3.8.0 -- Pan genome pipeline. website
• Salmon 0.7.2 -- Quantify abundances of transcripts from RNA-Seq data. website
• seqtk 1.2-r94 -- Tool for processing FASTA/FASTQ files. 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
• VSEARCH 2.3.4 -- USEARCH alternative for nucleotide alignment. website

·  anaconda/colsa -- A collection of the following bioinformatics software:

• Anaconda 4.3 -- Virtual environment manager for user pipelines. website
• FALCON-integrate 0.3.0 (falcon) -- Tools for long read consensus and assembly. website
• QIIME1 1.9.1 (qiime1) -- Pipeline for performing microbiome analysis. website
• QIIME2 2017.2.0 (qiime2) -- Pipeline for performing microbiome analysis. website

Thanks -

Toni Westbrook

Computational Scientist

Research Computing Center, College of Life Sciences and Agriculture

University of New Hampshire

Offices: 219 Morse Hall, 436 Gregg Hall