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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
http://sourceforge.net/projects/baccontigeditor/
A simple sequence alignment editing tool, written in Java.
Proper citation: BACContigEditor (RRID:SCR_001617) Copy
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
http://sourceforge.net/projects/mirprimer/
Software tool for automatic design of primers for PCR amplification of microRNAs using the method miR-specific RT-qPCR (Balcells, I., Cirera, S., and Busk, P.K. (2011). Specific and sensitive quantitative RT-PCR of miRNAs with DNA primers. BMC Biotechnol. 11, 70).
Proper citation: miRprimer (RRID:SCR_000480) Copy
http://sourceforge.net/projects/pyqpcr/
A GUI application written in python that deals with quantitative PCR (QPCR) raw data. Using quantification cycle values extracted from QPCR instruments, it uses a proven and universally applicable model to give finalized quantification resu
Proper citation: pyQPCR (RRID:SCR_000471) Copy
http://drfast.sourceforge.net/
A software which maps di-base reads (SOLiD color space reads) to reference genome assemblies in a fast and memory-efficient manner.
Proper citation: drFAST (RRID:SCR_000586) Copy
http://sourceforge.net/projects/gmcloser/
Software that fills and closes the gaps present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads. Unlike other gap-closing tools that use only NGS reads, GMcloser uses preassembled contig sets or long read sets as the sequences to close gaps and uses paired-end (PE) reads and a likelihood-based algorithm to improve the accuracy and efficiency of gap closure. The efficiency of gap closure can be increased by successive treatments with different contig sets.
Proper citation: GMcloser (RRID:SCR_000646) Copy
http://sourceforge.net/projects/detecttd/
Software tool to detect tandem duplications in sequencing reads. It is written in Python and requires NCBI Blast standalone.
Proper citation: detecttd (RRID:SCR_000681) Copy
http://sourceforge.net/projects/fastuniq/
A software tool for removal of de novo duplicates in paired short DNA sequences.
Proper citation: FastUniq (RRID:SCR_000682) Copy
http://sourceforge.net/projects/triagetools/
A collection of tools for partitioning raw data (fastq reads) from high-throughput sequencing projects. The tools are designed for basic data management as well for prioritizing analysis of certain subsets.
Proper citation: TriageTools (RRID:SCR_000675) 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
http://sourceforge.net/projects/operasf/
A sequence assembly software program that uses information from paired-end reads to optimally order and orient contigs assembled from shotgun-sequencing reads.
Proper citation: Opera (RRID:SCR_000665) Copy
http://sourceforge.net/projects/phaccs/
Software that gives estimates of the structure and diversity of uncultured viral communities using metagenomic information.
Proper citation: PHACCS (RRID:SCR_001232) Copy
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
http://biolemmatizer.sourceforge.net/
A domain-specific lemmatization software tool for the morphological analysis of biomedical literature.
Proper citation: BioLemmatizer (RRID:SCR_000117) Copy
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
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
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
http://sourceforge.net/projects/batman-seq/
A fast BWT-based short reads mapping tools which uses additional statistical method to model error profile of the sequencing experiment.
Proper citation: Batman-Seq (RRID:SCR_000048) Copy
http://sourceforge.net/projects/ms-spectre/
Software that provides (Quantitiave) analysis of multiple ls-ms(ms) runs, using mzXML import of raw data coming from spectrometers.
Proper citation: MS-Spectre (RRID:SCR_000266) Copy
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