Pipeline Pilot
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Application data |
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| Created by | Scott Markel |
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| Biological application domain(s) | Next Generation Sequencing, Gene expression analysis, Sequence analysis, SNP detection, ChIP-seq, RNA-Seq, Sequence assembly (de novo assembly), Genomics, Whole genome resequencing |
| Principal bioinformatics method(s) | Read mapping, Sequence analysis, Variant calling, Gene expression analysis, Comparative genomics, Sequence alignment |
| Technology | Sanger, Illumina, 454, ABI SOLiD |
| Created at | Accelrys |
| Maintained? | Yes |
| Input format(s) | Bowtie, BreakDancerMax, BWA, CisGenome, CNV-seq, Cufflinks, FASTQC, GATK, Integrative Genomics Viewer, MACS, Mapreads, MIRA3, MUMmer, SAMtools, snpEff, Tablet, TopHat, Velvet, tabix, Artemis, BioJava, BioPerl, BLAST, ClustalW, EMBOSS, HMMER, Jalview, MUSCLE, primer3, PROSITE, sim4 |
| Output format(s) | Circos, GBrowse2 |
| Software features | Integrated solution wrapping custom and third party tools for integration, analysis, and reporting |
| Programming language(s) | C++, Java, Perl, R, Pilot Script |
| Licence | Commercial |
| Operating system(s) | Linux, Windows |
Summary: Analysis and workflow development of Next Generation Sequencing and gene expression.
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Description
With the Next Generation Sequencing Collection you can perform comprehensive NGS analyses with a wide selection of popular algorithms, including methods for de novo assembly, mapping to reference sequences, identifying polymorphisms and structural variants (SNPs, insertions and deletions, and copy umber variations), measuring RNA expression levels (RNA-Seq), and identifying transcription factor binding sites (ChIP-seq).
With the Sequence Analysis Collection you can automate routine analysis of new sequence data, compare genes and genomes across species, integrate your own algorithms into any protocol, perform alignments with ClustalW or Muscle, build a hidden Markov model (HMM) from an alignment, perform similarity searching BLAST, PSI-BLAST or MegaBLAST, design siRNA protocols, annotate and manipulate sequences, integrate E-Utilities and run Entrez queries and databases into your analysis, create BLAST databases and FASTA "databases", perform integrated genomic-proteomics analyses with the Mass Spec for Proteomics Collection, perform chemo-genomic analyses with the Chemistry Collection.
With the Gene Expression Collection you can: analyze and annotate gene expression experiments, use BioConductor tools without performing programming or being familiar with the R package, easily create protocols to compare different analysis methods, integrate R/BioConductor analyses with analyses conducted with other Pipeline Pilot Collections, including the R Statistical calculation and Sequence Analysis collections, create comprehensive reports containing elements from both R graphics and the Reporting collection, download and analyze GEO data sets.
Links
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