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http://sourceforge.net/projects/cova/

A variant annotation and comparison tool for next-generation sequencing. It annotates the effects of variants on genes and compares those among multiple samples, which helps to pinpoint causal variation(s) relating to phenotype.

Proper citation: COVA (RRID:SCR_005175) Copy   

•   Source: SciCrunch Registry

http://bmda.cs.unibas.ch/HivHaploTyper/

Software for reconstructing haplotypes from next-generation sequencing data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PredictHaplo (RRID:SCR_005207) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/qure/

A software program for viral quasispecies reconstruction, specifically developed to analyze long read (>100 bp) next-generation sequencing (NGS) data. The software performs alignments of sequence fragments against a reference genome, finds an optimal division of the genome into sliding windows based on coverage and diversity and attempts to reconstruct all the individual sequences of the viral quasispecies--along with their prevalence--using a heuristic algorithm, which matches multinomial distributions of distinct viral variants overlapping across the genome division. QuRe comes with a built-in Poisson error correction method and a post-reconstruction probabilistic clustering, both parameterized on given error rates in homopolymeric and non-homopolymeric regions.

Proper citation: QuRe (RRID:SCR_005209) Copy   

•   Source: SciCrunch Registry

http://bioinfo.mc.vanderbilt.edu/VirusFinder/

Software tool for efficient and accurate detection of viruses and their integration sites in host genomes through next generation sequencing data. Specifically, it detects virus infection, co-infection with multiple viruses, virus integration sites in host genomes, as well as mutations in the virus genomes. It also facilitates virus discovery by reporting novel contigs, long sequences assembled from short reads that map neither to the host genome nor to the genomes of known viruses. VirusFinder 2 works with both paired-end and single-end data, unlike the previous 1.x versions that accepted only paired-end reads. The types of NGS data that VirusFinder 2 can deal with include whole genome sequencing (WGS), whole transcriptome sequencing (RNA-Seq), targeted sequencing data such as whole exome sequencing (WES) and ultra-deep amplicon sequencing.

Proper citation: VirusFinder (RRID:SCR_005205) Copy   

•   Source: SciCrunch Registry

http://rnaexpress.org/

Software designed as a user friendly solution to extract and annotate biologically important transcripts from next generation RNA sequencing data.

Proper citation: RNA-eXpress (RRID:SCR_005167) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.wistar.upenn.edu/isoformex

Software that estimates transcript expression levels and gene expression levels from mRNA-Seq data. Technically speaking, IsoformEx parses bowtie alignment files in a project directory (e.g. ~yourid/isoformex/xxx, where xxx is the project name) and generates two files: (1) xxx/xxx_transcript_1.txt: expression levels of all transcripts, (2) xxx/xxx_gene_1.txt: expression levels of all genes.

Proper citation: IsoformEx (RRID:SCR_005235) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/aldex/

RNA-seq tool that uses the Dirichlet distribution and a transformation to identify genes that exhibit small within-condition and large between-condition variance.

Proper citation: aldex (RRID:SCR_005110) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/cancer/cga/absolute

Software to estimate purity / ploidy, and from that compute absolute copy-number and mutation multiplicities. When DNA is extracted from an admixed population of cancer and normal cells, the information on absolute copy number per cancer cell is lost in the mixing. The purpose of ABSOLUTE is to re-extract these data from the mixed DNA population. This process begins by generation of segmented copy number data, which is input to the ABSOLUTE algorithm together with pre-computed models of recurrent cancer karyotypes and, optionally, allelic fraction values for somatic point mutations. The output of ABSOLUTE then provides re-extracted information on the absolute cellular copy number of local DNA segments and, for point mutations, the number of mutated alleles.

Proper citation: ABSOLUTE (RRID:SCR_005198) Copy   

•   Source: SciCrunch Registry

http://www.qcmg.org/bioinformatics/tiki-index.php

A single nucleotide variant caller optimised for identifying somatic variants in low cellularity cancer samples.

Proper citation: qSNP (RRID:SCR_005105) Copy   

•   Source: SciCrunch Registry

http://samtools.sourceforge.net/mpileup.shtml

Provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

Proper citation: SAMtools/BCFtools (RRID:SCR_005227) Copy   

•   Source: SciCrunch Registry

http://www.raetschlab.org/suppl/mitie

Software framework for simultaneous RNA-Seq-based Transcript Identification and Quantification in Multiple Samples. They define a likelihood function based on the negative binomial distribution, use a regularization approach to select a few transcripts collectively explaining the observed read data, and show how to find the optimal solution using Mixed Integer Programming. MiTie can a) take advantage of known transcripts, b) reconstruct and quantify transcripts simultaneously in multiple samples, as well as c) resolve the location of multi-mapping reads. It is designed for genome- and assembly-based transcriptome reconstruction.

Proper citation: MiTie (RRID:SCR_005228) Copy   

•   Source: SciCrunch Registry

http://orman.sourceforge.net/Home

A software tool for resolving multi-mappings within an RNA-Seq SAM file.

Proper citation: ORMAN (RRID:SCR_005188) Copy   

•   Source: SciCrunch Registry

https://github.com/vezzi/FRC_align

Software package containing tools to process bam files in order to evaluate and analyze de novo assembly / assemblers and identify Structural Variations suspicious genomics regions. The tools have been already successfully applied in several de novo and resequencing projects. This package contains two tools: # FRCbam: tool to compute Feature Response Curves in order to validate and rank assemblies and assemblers # FindTranslocations: tool to identify chromosomal rearrangements using Mate Pairs

Proper citation: FRCbam (RRID:SCR_005189) Copy   

•   Source: SciCrunch Registry

http://stothard.afns.ualberta.ca/downloads/NGS-SNP/

A collection of command-line scripts for providing rich annotations for SNPs identified by the sequencing of transcripts or whole genomes from organisms with reference sequences in Ensembl. Included among the annotations, several of which are not available from any existing SNP annotation tools, are the results of detailed comparisons with orthologous sequences. These comparisons allow, for example, SNPs to be sorted or filtered based on how drastically the SNP changes the score of a protein alignment. Other fields indicate the names of overlapping protein domains or features, and the conservation of both the SNP site and flanking regions. NCBI, Ensembl, and Uniprot IDs are provided for genes, transcripts, and proteins when applicable, along with Gene Ontology terms, a gene description, phenotypes linked to the gene, and an indication of whether the SNP is novel or known. A ?Model_Annotations? field provides several annotations obtained by transferring in silico the SNP to an orthologous gene, typically in a well-characterized species.

Proper citation: NGS-SNP (RRID:SCR_005182) Copy   

•   Source: SciCrunch Registry

http://omicslab.genetics.ac.cn/ISRNA/

An online toolkit for analyzing high-throughput small RNA sequencing data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ISRNA (RRID:SCR_009565) Copy   

•   Source: SciCrunch Registry

http://users-mb.au.dk/pmgrp/downloads.php

A pipeline for small RNA-seq data analysis.

Proper citation: shortran (RRID:SCR_009636) Copy   

•   Source: SciCrunch Registry

http://scalce.sourceforge.net/Home

A FASTQ compression tool that uses locally consistent parsing to obtain better compression rate.

Proper citation: SCALCE (RRID:SCR_009658) Copy   

•   Source: SciCrunch Registry

http://www.labmedmolge.unisa.it/inglese/research/imir

A modular pipeline for comprehensive analysis of smallRNA-Seq data, comprising specific tools for adapter trimming, quality filtering, DE analysis, target prediction by integrating multiple open source modules and resources in an automated workflow.

Proper citation: iMir (RRID:SCR_009496) Copy   

•   Source: SciCrunch Registry

http://www.stanford.edu/group/wonglab/SpliceMap/

A de novo splice junction discovery and alignment tool.

Proper citation: SpliceMap (RRID:SCR_009650) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry