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https://github.com/JialiUMassWengLab/TEMP
Software package for detecting transposable elements (TEs) insertions and excisions from pooled high-throughput sequencing data.
Proper citation: TEMP (RRID:SCR_001788) Copy
https://github.com/nicolazzie/AffyPipe
An open-source software pipeline for Affymetrix Axiom genotyping workflow.
Proper citation: AffyPipe (RRID:SCR_002032) Copy
https://github.com/adrlar/CanSNPer
Software that is a hierarchical genotype classifier of clonal pathogens.
Proper citation: CanSNPer (RRID:SCR_001980) Copy
http://sourceforge.net/projects/denovoassembler/files/
Software that assembles reads obtained with new sequencing technologies (Illumina, 454, SOLiD) using MPI 2.2.
Proper citation: Ray (RRID:SCR_001916) Copy
https://gemini.readthedocs.io/en/latest/
Framework for exploring genetic variation in the context of the genome annotations available for the human genome. Users can load a VCF file into a database and each variant is automatically annotated by comparing it to several genome annotations from source such as ENCODE tracks, UCSC tracks, OMIM, dbSNP, KEGG, and HPRD.
Proper citation: GEMINI (RRID:SCR_014819) Copy
https://laniakea-elixir-it.github.io/
Software tool for automatic deployment of virtual Galaxy environments for life science. Can be deployed over common cloud architectures supported both by public and private e-infrastructures. User interacts with Laniakea based service through simple front end that allows general setup of Galaxy instance, then Laniakea takes care of automatic deployment of virtual hardware and software components. User gains access with full administrative privileges to private, production grade, fully customized, Galaxy virtual instance, and to underlying virtual machine.
Proper citation: Laniakea (RRID:SCR_018146) Copy
Whole genome secondary analysis on Illumina sequencing platforms.
Proper citation: Isaac (RRID:SCR_012772) Copy
http://bioconductor.org/packages/release/bioc/html/lumi.html
Software that provides an integrated solution for the Illumina microarray data analysis.
Proper citation: lumi (RRID:SCR_012781) Copy
http://bioinf.comav.upv.es/ngs_backbone/index.html
A bioinformatic application created to work on sequence analysis by using NGS (Next Generation Sequencing) and sanger sequences.
Proper citation: Ngs backbone (RRID:SCR_012907) Copy
http://www.bioconductor.org/packages/release/bioc/html/rqubic.html
This software package implements the QUBIC algorithm for the qualitative biclustering with gene expression data.
Proper citation: rqubic (RRID:SCR_012869) Copy
http://bioconductor.org/packages/release/bioc/html/DiffBind.html
Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.
Proper citation: DiffBind (RRID:SCR_012918) Copy
http://www.bioconductor.org/packages/release/bioc/html/eisa.html
A biclustering method; it finds correlated blocks (transcription modules) in gene expression (or other tabular) data.
Proper citation: eisa (RRID:SCR_012883) Copy
http://sourceforge.net/projects/trowel-ec/
An error correction module for Illumina sequencing reads, which is based on the k-mer spectrum approach.
Proper citation: Trowel (RRID:SCR_012890) Copy
http://bioconductor.org/packages/release/bioc/html/CSAR.html
Statistical tools for the analysis of ChIP-seq data.
Proper citation: CSAR (RRID:SCR_012930) Copy
https://github.com/jstjohn/SeqPrep
A program to merge paired end Illumina reads that are overlapping into a single longer read.
Proper citation: SeqPrep (RRID:SCR_013004) Copy
http://www.bioconductor.org/packages/2.12/bioc/html/phyloseq.html
Software for handling and analysis of high-throughput microbiome census data.
Proper citation: phyloseq (RRID:SCR_013080) Copy
http://sourceforge.net/projects/amos/
A collection of tools and class interfaces for the assembly of DNA reads.
Proper citation: AMOS (RRID:SCR_013067) Copy
http://aluru-sun.ece.iastate.edu/doku.php?id=reptile
A software developed in C++ for correcting sequencing errors in short reads from next-gen sequencing platforms.
Proper citation: Reptile (RRID:SCR_013075) Copy
http://microbiomeutil.sourceforge.net/#A_CS
A chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500 bp).
Proper citation: ChimeraSlayer (RRID:SCR_013283) Copy
http://sourceforge.net/projects/telescoper/
An algorithm that iteratively extends long paths through a series of read-overlap graphs and evaluates them based on a statistical framework.
Proper citation: Telescoper (RRID:SCR_013206) Copy
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