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http://drive5.com/usearch/manual/uchime_algo.html
An algorithm for detecting chimeric sequences.
Proper citation: UCHIME (RRID:SCR_008057) Copy
http://cran.r-project.org/web/packages/RJaCGH/index.html
Software for Bayesian analysis of CGH microarrays fitting Hidden Markov Chain models.
Proper citation: RJaCGH (RRID:SCR_008381) Copy
http://www.cerc.utexas.edu/OnlineCall/
A fast basecalling scheme for Illumina''s Next Generation sequencing machines, specifically designed for GAII.
Proper citation: OnlineCall (RRID:SCR_008263) Copy
http://bioinfo.cipf.es/isacghtrac
Software to analyze CNV that will now normalize arrays CGH and it will visually integrate different genome annotations.
Proper citation: IsaCGH (RRID:SCR_008375) Copy
http://seqpig.sourceforge.net/
A software library for Apache Pig for the distributed analysis of large sequencing datasets on Hadoop clusters.
Proper citation: SeqPig (RRID:SCR_008548) Copy
http://mothra.ornl.gov/cgi-bin/cat/cat.cgi
A repository of tools for analysis and annotation of CAZYmes (Carbohydrate Active enZYmes)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: CAT (RRID:SCR_008421) Copy
http://www.broadinstitute.org/scientific-community/science/programs/cancer/ultrasome
An efficient methodology for detecting and delineating gains and losses of chromosomal material in DNA copy-number data.
Proper citation: Ultrasome (RRID:SCR_008465) Copy
http://pga.mgh.harvard.edu/oligopicker/
Software to help selecting up to five oligo probes for each of the DNA sequences you provided for microarray spotting.
Proper citation: OligoPicker (RRID:SCR_008720) Copy
http://dc.crs4.it/projects/biodoop
A suite of parallel bioinformatics applications based upon a popular open-source Java implementation of MapReduce, Hadoop.
Proper citation: Biodoop (RRID:SCR_008711) Copy
http://code.google.com/p/drgap/
Designed to identify Driver Genes and Pathways in cancer genome sequencing studies.
Proper citation: DrGaP (RRID:SCR_008670) Copy
http://www.broadinstitute.org/cancer/cga/invex/
A permutation-based method (written in Python) for ascertaining genes with a somatic mutation distribution showing evidence of positive selection for non-silent mutations.
Proper citation: InVEx (RRID:SCR_008734) Copy
http://www.ibridgenetwork.org/wustl/splinter
Software that detects and quantifies short IN/DELs as well as single nucleotide substitutions in pooled-DNA samples.
Proper citation: SPLINTER (RRID:SCR_005826) Copy
http://cran.r-project.org/web/packages/MetaQC/
Software for quality control and diagnosis for microarray meta-analysis. Quantitative quality control measures include: (1) internal homogeneity of co-expression structure among studies (internal quality control; IQC); (2) external consistency of co-expression structure correlating with pathway database (external quality control; EQC); (3) accuracy of differentially expressed gene detection (accuracy quality control; AQCg) or pathway identification (AQCp); (4) consistency of differential expression ranking in genes (consistency quality control; CQCg) or pathways (CQCp). For each quality control index, the p-values from statistical hypothesis testing are minus log transformed and PCA biplots were applied to assist visualization and decision. Results generate systematic suggestions to exclude problematic studies in microarray meta-analysis and potentially can be extended to GWAS or other types of genomic meta-analysis. The identified problematic studies can be scrutinized to identify technical and biological causes (e.g. sample size, platform, tissue collection, preprocessing etc) of their bad quality or irreproducibility for final inclusion / exclusion decision.
Proper citation: MetaQC (RRID:SCR_006000) Copy
http://www.bioconductor.org/packages/devel/bioc/html/deepSNV.html
Software package that provides quantitative variant callers for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. The algorithm is used for a comparative setup with a control experiment of the same loci and uses a beta-binomial model and a likelihood ratio test to discriminate sequencing errors and subclonal SNVs (single nucleotide variants).
Proper citation: deepSNV (RRID:SCR_006214) Copy
https://github.com/RGLab/pepStat
Software for statistical analysis of peptide microarrays. It uses an integrated analytical method for analyzing peptide microarray antibody binding data, from normalization through subject-specific positivity calls and data integration and visualization.
Proper citation: pepStat (RRID:SCR_006240) Copy
http://pathogenseq.lshtm.ac.uk/estmoi
A per-based software to estimate multiplicity of infection (MOI) in parasite genomic sequence data. It is primarily developed to address the limitations of current laboratory (PCR) based estimates of multiplicity using high throughput sequence data. It requires a BAM (alignment output of short reads to the reference genome), VCF (a file with information on variant calls) and FASTA (reference genome) files. # Short reads are aligned to a reference genome using BWA, BOWTIE, SMALT or other short read aligners to generate a BAM file. # Single Nucleotide Polymorphisms (SNPs) are then identified using SAMTools/BCFtools and stored in the VCF format. # The reference FASTA file is expected to be indexed using ''samtools faidx'' to generate a *.fai file. estMOI generates files containing MOI estimates for each SNP combinations (file with name *.log) and a summary for all chromosomes (file with name *.txt).
Proper citation: estMOI (RRID:SCR_006192) Copy
http://megasun.bch.umontreal.ca/People/lartillot/www/
A Bayesian Monte Carlo Markov Chain (MCMC) sampler software for phylogenetic reconstruction. Its main distinguishing feature is the underlying probabilistic model, CAT (Lartillot and Philippe, 2004). CAT is an infinite mixture model accounting for site-specific amino-acid or nucleotide preferences. It is well suited to phylogenomic studies using large multigene alignments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: PhyloBayes (RRID:SCR_006402) Copy
http://snps.ccbr.utoronto.ca:8080/SNPdryad/
Service to predict deleterious non-synonymous human Single Nucleotide Polymorphisms (SNPs) using only orthologous protein sequences.
Proper citation: SNPdryad (RRID:SCR_006414) Copy
http://cran.r-project.org/web/packages/QCGWAS/
Software tools for (automated and manual) quality control of the results of Genome Wide Association Studies.
Proper citation: QCGWAS (RRID:SCR_006408) Copy
http://sourceforge.net/projects/ngs-toolbox/
A collection of simple Perl scripts adressed to scientists doing research that bases on high throughput genomic/transcriptomic data. It does not require any bioinformatic expertise. The scripts perform fundamental processing steps like sorting sequences by TAGs, FASTQ to FASTA conversion, filtering and counting of redundant sequences, individually adjustable FASTQ quality filtering or basic analyses like base count and analysis of sequence length distribution.
Proper citation: NGS tools for the novice (RRID:SCR_000664) Copy
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