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http://bioinf.spbau.ru/quast

Quality assessment software tool for evaluating and comparing genome assemblies. It works both with and without a given reference genome. It produces many reports, summary tables and plots.

Proper citation: QUAST (RRID:SCR_001228) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/kanalyze/

A Java toolkit designed to convert DNA and RNA sequences into k-mers.

Proper citation: KAnalyze (RRID:SCR_001323) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/baccontigeditor/

A simple sequence alignment editing tool, written in Java.

Proper citation: BACContigEditor (RRID:SCR_001617) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/dnaclust/

Software program for clustering large number of short similar DNA sequences. It was originally designed for clustering targeted 16S rRNA pyrosequencing reads.

Proper citation: DNACLUST (RRID:SCR_001771) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/seqexpress/

A cross-platform software that estimates gene/isoform expression level via mRNA-Seq data. SeqExpress exams the Sequencing bias in mRNA-Seq and correct it to get more accurate estimation.

Proper citation: SeqExpress (RRID:SCR_004013) Copy   

•   Source: SciCrunch Registry

http://pythia.sourceforge.net/

Pythia is an open source thermodynamically oriented primer design python module. Pythia can be used in two ways. 1. Executable binaries only: under windows with cygwin and python 2.5 (built with mingw, that comes with the cygwin release). These executables allow the user to index DNA files for primer specificity search, design one primer pair per region, and tile regions with PCR amplicons. 2. A python module: under windows with cygwin, python2.5, numpy, swig, and mingw, or under linux with python2.4 or later, numpy, and swig (everything but numpy should be pre-installed on a normal linux system). The module gets you everything that the binaries get you, in a more pythonic framework. This package also includes modules for computing DNA binding and folding energies using the partition function approach with publicly available thermodynamic data. Usage documentation is in the downloads.

Proper citation: Pythia (RRID:SCR_004952) Copy   

•   Source: SciCrunch Registry

http://cortexassembler.sourceforge.net/index_cortex_var.html

A tool for genome assembly and variation analysis from sequence data. You can use it to discover and genotype variants on single or multiple haploid or diploid samples. If you have multiple samples, you can use Cortex to look specifically for variants that distinguish one set of samples (eg phenotype=X, cases, parents, tumour) from another set of samples (eg phenotype=Y, controls, child, normal). cortex_var features * Variant discovery by de novo assembly - no reference genome required * Supports multicoloured de Bruijn graphs - have multiple samples loaded into the same graph in different colours, and find variants that distinguish them. * Capable of calling SNPs, indels, inversions, complex variants, small haplotypes * Extremely accurate variant calling - see our paper for base-pair-resolution validation of entire alleles (rather than just breakpoints) of SNPs, indels and complex variants by comparison with fully sequenced (and finished) fosmids - a level of validation beyond that demanded of any other variant caller we are aware of - currently cortex_var is the most accurate variant caller for indels and complex variants. * Capable of aligning a reference genome to a graph and using that to call variants * Support for comparing cases/controls or phenotyped strains * Typical memory use: 1 high coverage human in under 80Gb of RAM, 1000 yeasts in under 64Gb RAM, 10 humans in under 256 Gb RAM

Proper citation: cortex var (RRID:SCR_005081) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/apps/mediawiki/amos/index.php?title=Bambus2

Software for scaffolding to address some of the challenges encountered when analyzing metagenomes. Scaffolding represents the task of ordering and orienting contigs by incorporating additional information about their relative placement along the genome. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with great flexibility in choosing the scaffolding parameters. In particular, Bambus is able to accept contig linking data other than specified by mate-pairs. Such sources of information include alignment to a reference genome (Bambus can directly use the output of MUMmer), physical mapping data, or information about gene synteny.

Proper citation: Bambus (RRID:SCR_005068) Copy   

•   Source: SciCrunch Registry

http://www.comp.hkbu.edu.hk/~chxw/software/G-BLASTN.html

A GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST. It can produce exactly the same results as NCBI-BLAST, and it also has very similar user commands. It also supports a pipeline mode, which can fully utilize the GPU and CPU resources when handling a batch of medium to large sized queries.

Proper citation: G-BLASTN (RRID:SCR_005062) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/viralfusionseq/

A versatile high-throughput sequencing (HTS) tool for discovering viral integration events and reconstruct fusion transcripts at single-base resolution. It combines soft-clipping information, read-pair analysis, and targeted de novo assembly to discover and annotate viral-human fusion events. A simple yet effective empirical statistical model is used to evaluate the quality of fusion breakpoints. Minimal user defined parameters are required.

Proper citation: VFS (RRID:SCR_005138) Copy   

•   Source: SciCrunch Registry

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://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://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

http://ergatis.sourceforge.net/

A web interface and scalable software system for bioinformatics workflows that is used to create, run, and monitor reusable computational analysis pipelines. It contains pre-built components for common bioinformatics analysis tasks. These components can be arranged graphically to form highly-configurable pipelines. Each analysis component supports multiple output formats, including the Bioinformatic Sequence Markup Language (BSML). The current implementation includes support for data loading into project databases following the CHADO schema, a highly normalized, community-supported schema for storage of biological annotation data. Ergatis uses the Workflow engine to process its work on a compute grid. Workflow provides an XML language and processing engine for specifying the steps of a computational pipeline. It provides detailed execution status and logging for process auditing, facilitates error recovery from point of failure, and is highly scalable with support for distributed computing environments. The XML format employed enables commands to be run serially, in parallel, and in any combination or nesting level.

Proper citation: Ergatis (RRID:SCR_005377) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/molbiolib/

A compact, portable, and extensively tested C++11 software framework and set of applications tailored to the demands of next-generation sequencing data and applicable to many other applications. It is designed to work with common file formats and data types used both in genomic analysis and general data analysis. A central relational-database-like Table class is a flexible and powerful object to intuitively represent and work with a wide variety of tabular datasets, ranging from alignment data to annotations. MolBioLib includes programs to perform a wide variety of analysis tasks such as computing read coverage, annotating genomic intervals, and novel peak calling with a wavelet algorithm. This package assumes fluency in both UNIX and C++.

Proper citation: MolBioLib (RRID:SCR_005372) Copy   

•   Source: SciCrunch Registry

http://splitread.sourceforge.net/

Software for detecting INDELs (small insertions and deletion with size less than 50bp) as well as large deletions that are within the coding regions from the exome sequencing data. It also can be applied to the whole genome sequencing data.

Proper citation: SPLITREAD (RRID:SCR_005264) Copy   

•   Source: SciCrunch Registry

http://biolemmatizer.sourceforge.net/

A domain-specific lemmatization software tool for the morphological analysis of biomedical literature.

Proper citation: BioLemmatizer (RRID:SCR_000117) Copy   

•   Source: SciCrunch Registry

http://soap.genomics.org.cn/soapfuse.html

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on August 23,2022. An open source tool developed for genome-wide detection of fusion transcripts from human being paired-end RNA-Seq data. This tool is a part of a larger set of tools to efficiently align oligonucleotides onto reference sequences .

Proper citation: SOAPfuse (RRID:SCR_000078) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/exomesuite/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software application designed to analyze variant call files from next generation sequencing data to identify variants causing disease.

Proper citation: exomeSuite (RRID:SCR_000129) Copy   

•   Source: SciCrunch Registry

https://github.com/lskatz/cg-pipeline

A software tool for assembling genome sequence data and running feature prediction and annotation tools on the assembly.

Proper citation: CG-Pipeline (RRID:SCR_000047) Copy   

•   Source: SciCrunch Registry