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http://www.allseq.com/default.aspx
Free online tools to find the best Sequencing Service provider for your project.
Proper citation: AllSeq (RRID:SCR_010053) Copy
http://dna.engr.uconn.edu/?page_id=105
Software package that can be used to infer isoform and gene expression levels from high-throughput transcriptome sequencing (RNA-Seq) data.
Proper citation: IsoEM (RRID:SCR_009993) Copy
http://code.google.com/p/bitseq/
A software application for inferring expression levels of individual transcripts from sequencing (RNA-Seq) data and estimating differential expression (DE) between conditions.
Proper citation: BitSeq (RRID:SCR_009904) Copy
http://bioen-compbio.bioen.illinois.edu/TrueSight/
Self-training Algorithm for Splice Junction Detection using RNA-seq.
Proper citation: TrueSight (RRID:SCR_009835) Copy
http://hkbic.cuhk.edu.hk/software/abmapper
A portable, easy-to-use package for spliced alignment, junction site detection, and reads mapping. The core module was written in C++ and wrapped in PERL scripts.
Proper citation: ABMapper (RRID:SCR_010242) Copy
http://htsvipr.sourceforge.net/
A software program to screen for sequence variants (SNPs, deletions) in sequence data generated by high-throughput-sequencing platforms.
Proper citation: vipR (RRID:SCR_010685) Copy
http://www.genome.umd.edu/masurca.html
A whole genome assembly software that combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: MaSuRCA (RRID:SCR_010691) Copy
http://bioinformatics.research.nicta.com.au/software/gossamer/
A software application for the de novo assembly of genomes from fragments of DNA that specifically attacks the question of scalability.
Proper citation: Gossamer (RRID:SCR_010612) Copy
http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0023501
An algorithm for de novo genome assembly with short paired-end reads.
Proper citation: Meraculous (RRID:SCR_010700) Copy
http://www.bio.ifi.lmu.de/contextmap
A context-based approach to identify the most likely mapping for RNA-seq experiments.
Proper citation: ContextMap (RRID:SCR_010496) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Integrated RNA-Seq read analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: CRAC (RRID:SCR_010652) Copy
http://wanglab.pcbi.upenn.edu/coral/
A machine learning software package that can predict the precursor class of small RNAs present in a high-throughput RNA-sequencing dataset. In addition to classification, it also produces information about the features that are most important for discriminating different populations of small non-coding RNAs.
Proper citation: CoRAL - Classification of RNAs by Analysis of Length (RRID:SCR_010828) Copy
http://paed.hku.hk/uploadarea/yangwl/html/software.html
A toolkit for prioritizing SNVs and indels from next-generation sequencing data.
Proper citation: PriVar (RRID:SCR_010784) Copy
http://compbio.cs.toronto.edu/CNVer/
A method for CNV detection that supplements the depth-of-coverage with paired-end mapping information, where matepairs mapping discordantly to the reference serve to indicate the presence of variation.
Proper citation: CNVer (RRID:SCR_010820) Copy
http://sv.gersteinlab.org/cnvnator/
An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.
Proper citation: CNVnator (RRID:SCR_010821) Copy
https://code.google.com/p/diplotyper/
A fully automated software tool which is available for Linux to investigate associations between a diplotype group and a phenotype in linear or logistic regression.
Proper citation: Diplotyper (RRID:SCR_010789) Copy
http://bioinfo-out.curie.fr/projects/freec/tutorial.html
Prediction of copy number alterations and loss of heterozygosity using deep-sequencing data.
Proper citation: Control-FREEC (RRID:SCR_010822) Copy
http://code.google.com/p/readdepth/
This package for R can detect copy number aberrations by measuring the depth of coverage obtained by massively parallel sequencing of the genome.
Proper citation: readDepth (RRID:SCR_010824) Copy
https://sites.google.com/site/vibansal/software/hapcut
A max-cut based algorithm for haplotype assembly using sequence reads from the two chromosomes of an individual.
Proper citation: HapCUT (RRID:SCR_010791) Copy
http://www.popgen.dk/software/index.php/Relate
Software providing a method that estimates the probability of sharing alleles identity by descent (IBD) across the genome and can also be used for mapping disease loci using distantly related individuals.
Proper citation: Relate (RRID:SCR_010794) Copy
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