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Ab Initio Tutorial.pdf Download Firefox

 
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MessagePosté le: Sam 3 Sep - 22:14 (2016)    Sujet du message: Ab Initio Tutorial.pdf Download Firefox Répondre en citant




Ab Initio Tutorial.pdf Download Firefox > urlin.us/3zltq







Ab Initio Tutorial.pdf Download Firefox

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Need X11 support to run GUI Depends on java Depends on phyml KAAS - KEGG Automatic Annotation Server module name: KAAS version 2.0 Functional annotation of genes by BLAST comparisons against the manually curated KEGG GENES database To use: review instructions at /group/bioinfo/apps/apps/KAAS-2.0/readme.txt Then, copy /group/bioinfo/apps/apps/KAAS-2.0/kaas.config to your working directory Issue all KAAS commands from that directory Depends on ruby Depends on perl Depends on HMMER Depends on blast/2.2.26 khmer module name: khmer version 2012-07-06 In-memory k-mer counting Info in /group/bioinfo/apps/apps/khmer-2012-07-06/doc Forum: khmer is *pre-publication* and *research* software Depends on biopython/2.7.2 KmerGenie module name: kmergenie version 1.5692 Estimates the best k-mer length for de novo assembly Depends on R-bioconductor Depends on biopython/2.7.3 LRNAscaffolder module name: LRNAscaffolder version 14Feb2014 Long transcriptome reads to scaffold genome Manual: Depends on gcc Depends on perl/5.18.1 LAPACK Linear Algebra PACKage and BLAS module name: lapack version 3.4.2 compiled with gcc 4.7.2 Depends on gcc libgcrypt module name: libgcrypt version 1.5.3 General purpose cryptographic library Depends on libgpg-error libxml2 module name: libxml2 version 2.9.1 XML C parser and toolkit developed for the Gnome project Depends on gcc libxslt module name: libxslt version 1.1.28 XSLT C library developed for the GNOME project XSLT is a an XML language to define transformation for XML Depends on gcc Depends on libxml2 Lucy module name: lucy version 1.20p DNA sequence quality and vector trimming tool Manual: man lucy Depends on gcc lz4 module name: lz4 version 122 Extremely Fast Compression algorithm man lz4 Depends on gcc MACS module name: macs version 2.1.0 Other versions: 1.4.2a, 1.4.2b, 2.0.10, 2.0.10-2.7.2 Model-based Analysis for ChIP-Seq Info: /group/bioinfo/apps/apps/MACS-2.1.0/README.rst Depends on biopython/2.7.8 Depends on PeakSplitter MAFFT module name: mafft version 6.903 Multiple alignment program for amino acid or nucleotide sequences man pages for mafft and mafft-homologs MAKER module name: MAKER version 2.10 Other versions: 2.27b, 2.28b, 2.30p, 2.31.7 Genome annotation pipeline Info: Info: /group/bioinfo/apps/apps/MAKER-2.10/README Tutorial: Forum: Depends on perl Depends on SNAP Depends on RepeatMasker Depends on exonerate Depends on blast/2.2.26 Depends on AUGUSTUS Depends on GeneMark Depends on mpich2/1.4.1p1gcc-4.7.2 MAQ module name: maq version 0.7.1 MAQ: Mapping and Assembly with Qualities Manual: FAQ: Depends on gcc MaSuRCA (Maryland Super Read Cabog Assembler) module name: MaSuRCA version 2.1.0 Genome assembler ftp://ftp.genome.umd.edu/pub/MaSuRCA/ Manual: /group/bioinfo/apps/apps/MaSuRCA-2.1.0/doc/MaSuRCAQuickStartGuide.txt Manual: /group/bioinfo/apps/apps/MaSuRCA-2.1.0/doc/MaSuRCAQuickStartGuide.pdf Need to copy /group/bioinfo/apps/apps/MaSuRCA-2.1.0/srconfigexample.txt into assembly directory and modify as needed Depends on gcc Depends on perl MATLAB Compiler Runtime (MCR) module name: MCR version 7.14 Shared libraries that enables the execution of compiled MATLAB applications Corresponds to MATLAB R2010b matrix2png module name: matrix2png version 1.2.2 Visualizations of microarray data and many other data types Manual at Examples at Depends on gcc Mauve module name: mauve version 2.3.1 Construct multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion Manual: Manual: /group/bioinfo/apps/apps/mauve2.3.1/mauveuserguide.pdf Note: Needs X11 support for GUI (not needed with command line utilities mauveAligner or progressiveMauve) Depends on java mcl module name: mcl version 12-068 The Markov Cluster Algorithm (MCL) MCL algorithm finds cluster structure in graphs man pages available Depends on gcc MeDUSA module name: medusa version 1.0 Pipeline for MeDIP-seq data analysis Info at /group/bioinfo/apps/apps/medusa-1.0/README Copy and change the config file in /group/bioinfo/apps/apps/medusa-1.0/configfiles/medusatemplate.cfg Depends on perl Depends on R-bioconductor Depends on bwa Depends on samtools Depends on fastqc Depends on USeq Depends on BEDTools MEGAN (MEtaGenome ANalyzer) module name: MEGAN version 5.2.3 Other versions: 4.70.4, 5.1.4 Software for analyzing metagenomes Release Notes: Need X11 support for program to run (ssh -X) Need license key from Depends on java MeQA module name: MeQA version 1.0.0 A pipeline for MeDIP-seq data quality assessment and analysis Need to copy /group/bioinfo/apps/apps/MeQA-1.0.0/example-config.cfg to your project dir and modify to suit your needs Depends on R-bioconductor Depends on biopython/2.7.2 Depends on bwa Depends on samtools Depends on BEDTools Depends on samstat Depends on CEAS MetaCV module name: metacv version 2.2.9 Composition based classification for short metagenomic sequences Manual: /group/bioinfo/apps/apps/metacv-2.2.9/MetaCVmanual.pdf Need to install prokaryotes database from website (>16GB compressed) Depends on gcc MetaVelvet module name: MetaVelvet version 1.2.01 A short read assember for metagenomics Built with MAX KMER LENGTH=99 and CATEGORIES=4 Depends on velvet METIS module name: metis version 5.0.2 Serial Graph Partitioning and Fill-reducing Matrix Ordering Manual: Manual: /group/bioinfo/apps/apps/metis-5.0.2/manual/manual.pdf Depends on gcc Microbiome Utilities Portal of the Broad Institute module name: microbiomeutil version r20110519 Provides microbiome utilities : - Sequence alignment (NAST-iEr) - Chimera detection (ChimeraSlayer, WigeoN) - Operational taxonomic unit OTU binning (TreeChopper) - Sequence assembly (AmosCmp16Spipeline) - database of reference 16S sequences Info: /group/bioinfo/apps/apps/microbiomeutil-r20110519/docs Depends on blast/2.2.26 Depends on cdbtools MicroRazerS module name: MicroRazerS version 1.0 Fast mapping short RNAs onto a reference genome Mailing list: Depends on gcc Minia module name: minia version 1.5418 Other versions: 1.5418-maxk128, maxk128, maxk32 Short-read assembler based on a de Bruijn graph Manual: /group/bioinfo/apps/apps/minia-1.5418/manual.pdf This version is compiled with support for maximum k-mer size of 32 Depends on gcc MIRA module name: mira version 4.0.2 Other versions: 3.4.1.1, 3.9.1, 3.9.10, 3.9.11, 3.9.12, 3.9.14, 3.9.15, 3.9.16, 3.9.18, 3.9.3, 3.9.4, 3.9.5, 3.9.7, 3.9.8, 3.9.9, 4.0, 4.0.1, 4.0rc1, 4.0rc2, 4.0rc3, 4.0rc4, 4.0rc5, 4.9.1, 4.9.3 Whole genome shotgun and EST sequence assembler Manual at Docs at /group/bioinfo/apps/apps/mira-4.0.2/docs Mailing lists: Depends on gcc Depends on tcl miRDeep module name: mirdeep version 2.0.0.4 Discovering known and novel miRNAs from deep sequencing data Manual at Depends on perl Depends on bowtie Depends on ViennaRNA Depends on randfold miRDeep-P module name: miRDeep-P version 1.3 A computational tool for analyzing the microRNA transcriptome in plants Manual at Manual at /group/bioinfo/apps/apps/miRDP-1.3/miRDPmanual1.3.pdf Depends on perl Depends on bowtie Depends on ViennaRNA Depends on randfold MIREAP module name: mireap version 0.2 Reap miRNAs from deeply sequenced smRNA library Depends on perl Depends on ViennaRNA miRExpress module name: miRExpress version 2.1.3 Analyzing high-throughput sequencing data for profiling microRNA expression Usage: /group/bioinfo/apps/apps/miRExpress-2.1.3/README Includes data from miRBase 18.0 (2012APR27) Depends on gcc miRNAkey module name: miRNAkey version 1.2 A pipeline microRNA Deep Sequencing data analysis Manual: Need to copy /group/bioinfo/apps/apps/miRNAkey-1.2 to your project directory and run from there Depends on java Depends on bwa Depends on fastx Depends on perl MITObim module name: MITObim version 1.7 Other versions: 1.6 Mitochondrial baiting and iterative mapping Version 1.7 uses mira 4.0.x Info: /group/bioinfo/apps/apps/MITObim-1.7/README.md Test data: /group/bioinfo/apps/apps/MITObim-1.7/testdata1.tgz Depends on perl Depends on mira MOTHUR module name: mothur version 1.34.4 Other versions: 1.25.0, 1.25.1, 1.32.1 Microbial ecology tools mothur and uchime (not GUI version) wiki: forum: Depends on gcc MrBayes module name: mrbayes version 3.2.1 Bayesian Inference of Phylogeny Manual at Depends on beagle Mugsy module name: Mugsy version 1r2.3 Multiple whole genome alignment tool Depends on gcc Depends on muscle MUMmer module name: MUMmer version 3.23 Ultra-fast alignment of large-scale DNA and protein sequences Manual: Tutorial: Info: /group/bioinfo/apps/apps/MUMmer-3.23/docs Depends on gcc MUSCLE module name: muscle version 3.8.31 Other versions: 3.8.425 Multiple sequence alignment (faster than clustalw) Docs: MySQL Connector/J module name: mysql-connector-java version 5.1.21 Other versions: 5.0.5, 5.0.8 MySQL Connector/J is the official JDBC driver for MySQL Docs: /group/bioinfo/apps/apps/mysql-connector-java-5.1.21/docs Depends on java NCBI BLAST module name: blast version 2.2.30+ Other versions: 2.2.22, 2.2.25+, 2.2.26, 2.2.26+, 2.2.27+, 2.2.28+, 2.2.29+ Basic Local Alignment Search Tool Manuals: Release notes: Depends on gcc NCBI BLAST CGI programs module name: wwwblast version 2.2.26 BLAST CGI programs (legacy version) Docs: /group/bioinfo/apps/apps/wwwblast-2.2.26/docs This "legacy" version of NCBI BLAST is deprecated; see for reasons to use BLAST+ instead These are the wwwblast CGI programs. 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