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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.bcgsc.ca/platform/bioinfo/software/abyss
Software providing de novo, parallel, paired-end sequence assembler that is designed for short reads. ABySS 1.0 originally showed that assembling human genome using short 50 bp sequencing reads was possible by aggregating half terabyte of compute memory needed over several computers using standardized message passing system. ABySS 2.0 is Resource Efficient Assembly of Large Genomes using Bloom Filter. ABySS 2.0 departs from MPI and instead implements algorithms that employ Bloom filter, probabilistic data structure, to represent de Bruijn graph and reduce memory requirements.
Proper citation: ABySS (RRID:SCR_010709) 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
Software package for sequence alignment, assembly and analysis. Integrated and extendable desktop software platform for organization and analysis of sequence data. Bioinformatics software platform packed with molecular biology and sequence analysis tools.
Proper citation: Geneious (RRID:SCR_010519) Copy
http://mirtar.mbc.nctu.edu.tw/human/
An integrated web server for identifying miRNA-target interactions in human. The tool enables biologists easily to identify the biological functions and regulatory relationships between a group of known/putative miRNAs and protein coding genes. It also provides perspective of information on the miRNA targets on alternatively spliced transcripts.
Proper citation: miRTar (RRID:SCR_010851) 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
http://rth.dk/resources/rnasnp/
Software / Web Server to predict the effect of SNPs on local RNA secondary structure based on the RNA folding algorithms implemented in the Vienna RNA package.
Proper citation: RNAsnp (RRID:SCR_010837) Copy
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