[Colsa-premise-users] QIIME, New Software, Data Files
Westbrook, Anthony S
Anthony.Westbrook at unh.edu
Mon Mar 6 13:12:53 EST 2017
Hi Everyone -
A new batch of software has been installed on premise. The full list is included at the end of this email.
Additionally, both the QIIME and QIIME2 pipeline packages have been installed. Due to installation requirements, they are run in a different manner than other COLSA premise software:
1. Unload the linuxbrew/colsa module (if loaded): "module unload linuxbrew/colsa"
2. Load the anaconda/colsa module: "module load anaconda/colsa"
3. Activate the desired QIIME environment: "source activate qiime1" or "source activate qiime2"
4. Execute the desired QIIME commands
5. When done:
* If finished with session, simply logout
* To continue working with other COLSA software, deactivate the QIIME environment: "source deactivate"
* Unload anaconda module: "module unload anaconda/colsa"
Also, we've gotten a few requests on where program-packaged data files (such as Augustus's config/profile/model files) are located on premise. These can usually be found in the following location:
/mnt/lustre/software/linuxbrew/colsa/Cellar/<PROGRAM NAME>/<VERSION>/
Often, they will be located in the "libexec" subdirectory in this location. Note, these directories are read only. If you require modifying a file (such as a customized configuration file), copy the file into your home directory and instruct the application to make use of this location.
The newest software list is as follows:
* linuxbrew/colsa -- A collection of the following bioinformatics software:
* ABySS 2.0.2 -- Paired-end short read sequence assembler. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.bcgsc.ca_platform_bioinfo_software_abyss&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=VWUcLVi27DGUx4cUAWwtwVGrjEzvCgtkqlSgu5a2AIU&e= >
* ARAGORN 1.2.36 -- Detection of tRNA and tmRNA in nucleotide sequences. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__mbio-2Dserv2.mbioekol.lu.se_ARAGORN&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=BEdNfMY-_qWvxQUohdcXC8BiOEI9RTTkf7SvcPp4wOw&e= >
* Augustus 3.2.2 -- Gene prediction in eukaryotic genomic sequences. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__bioinf.uni-2Dgreifswald.de_augustus_&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=TPxiuHRBhq0iNjubnf5i0fgDVwmev7Q-gmgaxmDVGhU&e= >
* BamTools 2.4.0 -- Toolkit for working with BAM (Binary Alignment Map) data. website<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_pezmaster31_bamtools&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=NV5YJ_TwkV_EAIRXkF6P8lOXB0jxdDTFl-HuidwluYE&e= >
* Barrnap 0.7 -- Rapid ribosomal RNA predictor. website<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_tseemann_barrnap&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=FHvgpyO9sMrzHpky7KfS57WafP_wvTf_1p_oKSq7tUY&e= >
* BayeScan 2.0 -- Detecting natural selection from population-based genetic data. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__cmpg.unibe.ch_software_BayeScan_&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=_EgfYxY4b3yUihqDbwP_DFO4uLYpIN18CDsAKC2ulDY&e= >
* BedTools 2.26.0 -- Toolkit for performing a variety of genomics analysis tasks. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__bedtools.readthedocs.io_en_latest_&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=0oc0oQpYP9A23KkXsaAqPecDoo2GhZHccpgJCqZCywI&e= >
* BFC r181 -- Illumina read error correction website<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_lh3_bfc&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=E1bok_D4adYHOUdgVw53pVUAVTpn5bcfj9jocpdufFs&e= >
* BLAST Suite 2.5.0 -- Nucleotide/Protein alignment against nucleotide/protein references. website<https://urldefense.proofpoint.com/v2/url?u=https-3A__blast.ncbi.nlm.nih.gov_Blast.cgi-3FPAGE-5FTYPE-3DBlastDocs-26DOC-5FTYPE-3DDownload&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=iTkYtLmpv7SV8tEljgfEmjKUP5_Aw4MEA8GFSXuK-ZM&e= >
* Bowtie 1.1.2 -- Nucleotide (<50 bp) alignment against nucleotide references. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__bowtie-2Dbio.sourceforge.net_index.shtml&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=d4dXpYihgGCCVeZi875DNHbuylS3v1EsrjO0cqfgTtQ&e= >
* Bowtie 2 2.2.9 -- Nucleotide (>50 bp) alignment against nucleotide references. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__bowtie-2Dbio.sourceforge.net_bowtie2_index.shtml&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=XmnBwZUxo2jyhn4KTqwrNxv0BFIMEi0VFeijooU90IE&e= >
* BUSCO 1.22 -- Assessment of genome assemblies, gene sets, and transcriptome completeness. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__busco.ezlab.org_&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=YsXVdfp6XTm8HfBg43Ley5USryGEXQPZ8-8CuK6hKFc&e= >
* BWA 0.7.15 -- Nucleotide alignment against nucleotide references. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__bio-2Dbwa.sourceforge.net_&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=HfalLXt8n1yBtYxsr9VN9j43agU5kyCG5awYDBl0zYA&e= >
* Canu 1.4 -- High-noise, single-molecule (PacBio RS II / Oxford Nanopore MinION) assembler. website<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_marbl_canu&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=OAIDdReXjBfk-nZ_zwktCTB_zAXO0wKQLgiKAXAq5Is&e= >
* CD-HIT 4.6 -- Nucleotide and protein cluster creation and comparison. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__weizhongli-2Dlab.org_cd-2Dhit_&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=2ihCiIcMDED8CTeqiR4r-Od63zyUOGwVpH7hm-3H3nU&e= >
* dammit 0.3.2 -- De novo transcriptome annotator. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__dammit.readthedocs.io_en_latest_index.html&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=6aXIc6yd72ur1WKZTudITnrjdL6Bs-9koOZe-E22ikY&e= >
* E-MEM 1.0.0 -- Compute MEMs (maximal exact matches) between large genomes. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.csd.uwo.ca_-257Eilie_E-2DMEM_&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=MeJrfFbbGOO8R2179j6NLCxa4d3-7HKAdIww0vp5RKQ&e= >
* EMBOSS 6.6.0.0 -- Toolkit containing multiple applications for molecular biology analysis. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__emboss.sourceforge.net_index.html&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=EowX4kELdId3XsoOYYItlyTm-8sAwKYhOvFn47OemXU&e= >
* ExaBayes 1.5 -- Bayesian inference of phylogeny for computer clusters. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__sco.h-2Dits.org_exelixis_web_software_exabayes_&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=KQOX3qSJLsYOfjF2LDVhqFBWt6iCxFH6fHZSz-DzvYo&e= >
* Exonerate 2.2.0 -- Nucleotide and protein alignment against nucleotide and protein references. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ebi.ac.uk_about_vertebrate-2Dgenomics_software_exonerate&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=uzMRLIJc33HyIFmkR6CIj48Me8d_c0naR-AjQb5TVhU&e= >
* FastQC 0.11.5 -- Quality control reporting tool for sequence data. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.bioinformatics.babraham.ac.uk_projects_fastqc_&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=QhG5M3usCREbVQVeacQ_avGHZBvRdCNmi4mCT6v5n4I&e= >
* FASTX-Toolkit 0.0.14 -- Collection of tools for short-read FASTA/FASTQ files. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__hannonlab.cshl.edu_fastx-5Ftoolkit_&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=TVTbl6wsaYPg6i4XTyoIJjZtYoRcKaDi-tNZOvGHWvI&e= >
* HMMER 3.1b2 -- Homolog search and sequence alignment using hidden Markov models. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__hmmer.org_&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=hBH1MM8J8Xz_eP1e1FQ5c94_hBvir9DsUkM7gnaSMFw&e= >
* Infernal 1.1.2 -- Inference of RNA alignments. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__eddylab.org_infernal_&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=XbEiafGqd8dpL5FLX2J509jYZWI8018eAok3rBNjyno&e= >
* Jellyfish 2.2.6 -- K-mer counting and analysis. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.genome.umd.edu_jellyfish.html&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=wbGpjJOrQwNvTpMSGweTLdksOf0YIpi72ks2WzYVzrE&e= >
* Kallisto 0.43.0 -- Quantify abundances of transcripts from RNA-Seq data. website<https://urldefense.proofpoint.com/v2/url?u=https-3A__pachterlab.github.io_kallisto_about.html&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=FCUpO3bir60KmpUe-lxrRob826TT22MkCBh1KxwJhTQ&e= >
* MAFFT 7.305b -- Nucleotide/Protein multiple sequence alignment. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__mafft.cbrc.jp_alignment_software_&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=uoU5cjTBjIwigoSqsOhOlNyR-CUynbAbnO6QJCHNXA8&e= >
* Maker 2.31.9 -- Annotation of prokaryotic/eukaryotic genomes. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.yandell-2Dlab.org_software_maker.html&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=ipnwyQJ_F5RSuCc2taoA4vgKO2VEqYX7uo3h3F_cW0E&e= >
* MinCED 0.2.0 -- Find CRISPRs in shotgun DNA sequences or full genomes. website<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ctSkennerton_minced&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=zps-NfLAU8wRrat2QTVuRPVNPEuC92yhckdO9Sq7u_g&e= >
* MCL 14-137 -- Unsupervised cluster algorithm for graphs (Markov Cluster Algorithm). website<https://urldefense.proofpoint.com/v2/url?u=http-3A__http-3A_micans.org_mcl_&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=PYNU89Sk_1mPsyVkOUCerd5jOPL0MaE4ZwJalBTrtW0&e= >
* MrBayes 3.2.6 -- Bayesian inference of phylogeny. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__mrbayes.sourceforge.net_&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=ogSmvydek8IGeSKlYSZCG0QDzwiHJb-x373PahMKu1I&e= >
* MUSCLE 3.8.1551 -- Nucleotide/Protein multiple sequence alignment. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.drive5.com_muscle_&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=4W5htbx5X7rG6vH3vo79QiEW1FE0izBiunt6cIPXbg8&e= >
* PALADIN 1.3.2 -- Nucleotide alignment and UniProt reporting against annotated nucleotide/transcriptome/protein references. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__github.com_twestbrookunh_paladin&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=Y24mHz20l_p3UVh7APp15Erc4F1VxYtmhFQ-r_0nPcY&e= >
* PALADIN-plugins 1.0.0 -- Pipeline for PALADIN related analysis. website<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_twestbrookunh_paladin-2Dplugins&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=uxqoGfWrxCkST1Gl8ES9wYkDN9bAR5uFY4T_YBXb40s&e= >
* PEAR 0.9.10 -- Illumina Paired-end read merger. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__sco.h-2Dits.org_exelixis_web_software_pear_&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=S6zMkB-yFNcdnpUh3Anj2Do49vT17egkreBcIeDK-eg&e= >
* Perl 5.24.0 -- Perl programming language. website<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.perl.org_&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=YiBnJ6s_kzBAO5gv-87cNuRTbICHtYd-JhMAamQK2Ak&e= >
* Plink 1.07 -- Whole genome data analysis toolset. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__pngu.mgh.harvard.edu_-257Epurcell_plink_index.shtml&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=NBCqpypk_wMrUMsbP7KFFACq-cksQLGP1IAQ3Tgd6jc&e= >
* PRANK 140603 -- Probabilistic multiple sequence alignment for closely related sequences. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ebi.ac.uk_research_goldman_software_prank&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=J7U66gAkq8m8J_AAyeoa8k-ltcpHGgDHpHQBXL-9iNE&e= >
* PRODIGAL 2.6.2 -- Microbial gene finder. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__prodigal.ornl.gov_&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=Yugh5NA51riTlqynVDaS1FVI9-TlvYsrvWuJXh6kMro&e= >
* Prokka 1.11_1 -- Annotation of prokaryotic genomes. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.vicbioinformatics.com_software.prokka.shtml&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=c0IGOZ6gIIvuiW2s_CCXhIyEwJ9eV4ddOp2W1IlLkC8&e= >
* Python 2 2.7.13 -- Python programming language. website<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.python.org_&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=MmNAJXIUSgHsXknxeJSbYQElHDcWpvgBrb1Bb1_eV78&e= >
* Python 3 3.6.0 -- Python programming language. website<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.python.org_&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=MmNAJXIUSgHsXknxeJSbYQElHDcWpvgBrb1Bb1_eV78&e= >
* QUAST 4.4.1 -- Quality assessment of genome assemblies. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__bioinf.spbau.ru_quast&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=nmMW_d0mbmN-4X24YEGhLIqR_w4Anw21TijKyHrhO5Y&e= >
* QuorUM 1.0.0 -- Illumina read error correction. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.genome.umd.edu_quorum.html&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=h3PJ2DY5ZsKG-IocOC9vtFMPg-X8KOfPq_DUs8giRKo&e= >
* R 3.3.2 -- R programing language. website<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.r-2Dproject.org_&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=s-86DiAs--M234AcoGpjS-nn88VopbZP_ZaPpVxU77Q&e= >
* RAxML 8.2.9 -- Maximum-Likelihood inference of phylogeny. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__sco.h-2Dits.org_exelixis_web_software_raxml_index.html&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=3Zt5w6rAU4QDi55PfSgN-Q28YXLFrwn1GhPTlWtm6f0&e= >
* Rcorrector 1.0.2 -- Illumina RNA-seq error correction. website<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_mourisl_Rcorrector&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=-p79gU58r0UwpVxE39BML9sHNjYYDfkDu5Q1ck1UQJA&e= >
* Repeatmasker 4.0.5 -- DNA repeat and low complexity detection. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.repeatmasker.org_&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=w2Ly8eaee3sCiq4ZRjixYaV0D3x0hPmNC6KwzlrDQYk&e= >
* Roary 3.8.0 -- Pan genome pipeline. website<https://urldefense.proofpoint.com/v2/url?u=https-3A__sanger-2Dpathogens.github.io_Roary_&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=XagB52wlbP1DF620ZM3c0LmxWO-eh4h0VADMEajjvM8&e= >
* Salmon 0.7.2 -- Quantify abundances of transcripts from RNA-Seq data. website<https://urldefense.proofpoint.com/v2/url?u=https-3A__combine-2Dlab.github.io_salmon&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=8i77VML4EdUVTpg1HgjD1oJejR7isFUFkqSVSscr4ss&e= >
* seqtk 1.2-r94 -- Tool for processing FASTA/FASTQ files. website<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_lh3_seqtk&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=FB195tA9BOUI1JkJyNdE2HYOwyoXDfgb-BVOn1X57lk&e= >
* Skewer 0.2.2 -- Adapter trimmer for paired-end reads. website<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_relipmoc_skewer&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=FifvNtuh4ZY-8iSmO690GkFy8eqPAmfRZOOvS2OAPnk&e= >
* SNAP 2013-11-29 -- Semi-HMM-based gene prediction tool. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__korflab.ucdavis.edu_software.html&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=VBfcuhGiTOHf6J8UbyuSMs-JESDOBNdcQf2gz0UtHs8&e= >
* SPAdes 3.9.0 -- Small genome assembly toolkit. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__cab.spbu.ru_software_spades_&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=-39BfQcplzS4xohOg6KhKJ4CCnP8SjvMgmwfN-kgO_A&e= >
* Transdecoder 3.0.1 -- Identify candidate coding regions within transcripts. website<https://urldefense.proofpoint.com/v2/url?u=https-3A__transdecoder.github.io_&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=nXx79rfD-fGLBIyGm9ALLCq8-jdWyuDehEb2gQ6D5eQ&e= >
* Trimmomatic 0.36 -- Illumina read trimming tool. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.usadellab.org_cms_-3Fpage-3Dtrimmomatic&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=k9V7e4X6dGXZuE5wru7pFb1n64E-rRalYkeyvYrTH2U&e= >
* Trinity 2.3.2 -- Illumina RNA-seq read sequence assembler. website<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_trinityrnaseq_trinityrnaseq_wiki&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=OhOwrBES7mFlAAcnZJG1CIiJyj7l35LGQB4F_6WYoxg&e= >
* VSEARCH 2.3.4 -- USEARCH alternative for nucleotide alignment. website<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_torognes_vsearch&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=nKi2BZcAbbGI1VYW50RtZhXFf16tKcfBJYbIcz18Ijw&e= >
* anaconda/colsa -- A collection of the following bioinformatics software:
* QIIME1 1.9.1 -- Pipeline for performing microbiome analysis. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__qiime.org&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=KaXT4Rjrb5Aq4SrzdFkVRD3Eq878MDacR1ZsobEB918&e= >
* QIIME2 2017.2.0 -- Pipeline for performing microbiome analysis. website<https://urldefense.proofpoint.com/v2/url?u=http-3A__qiime2.org&d=DwIFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=8HYwVFqhnt1sFxxpNmhS3rDbt5VWyVyex3AUIRkGrP3ToENh47_e6npSnUj4m4_x&m=YiXcBNxsG_4DU86ZYJdkfaYHZdFT6BtWZukrfU0a4aQ&s=4tYvQGQKgDjEe2EtpsIe2Vx7WEEEPjbNuKtBhw5WNaU&e= >
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
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