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http://www.broadinstitute.org/software/syzygy/

A targeted sequencing post processing analysis software tool that allows: 1. SNP and indel detection; 2. Allele frequency estimation; 3. Single-marker association test; 4. Group-wise marker test association; 5. Experimental QC summary (%dbSNP, Ts/Tv, Ns/S); 6. Power to detect variant. (entry from Genetic Analysis Software)

Proper citation: SYZYGY (RRID:SCR_002157) Copy   

•   Source: SciCrunch Registry

http://ngsutils.org/

A suite of software tools for analyzing and manipulating next-generation sequencing datasets, such as FASTQ, BED and BAM format files. These tools provide a stable and modular platform for data management and analysis.

Proper citation: NGSUtils (RRID:SCR_001236) Copy   

•   Source: SciCrunch Registry

http://khmer.readthedocs.org/

Software library and suite of command line tools for working with DNA sequence that takes a k-mer-centric approach to sequence analysis. It is primarily aimed at short-read sequencing data such as that produced by the Illumina platform.

Proper citation: khmer (RRID:SCR_001156) Copy   

•   Source: SciCrunch Registry

http://faculty.washington.edu/browning/beagle/beagle.html

Software package for analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples. BEAGLE can * phase genotype data (i.e. infer haplotypes) for unrelated individuals, parent-offspring pairs, and parent-offspring trios. * infer sporadic missing genotype data. * impute ungenotyped markers that have been genotyped in a reference panel. * perform single marker and haplotypic association analysis. * detect genetic regions that are homozygous-by-descent in an individual or identical-by-descent in pairs of individuals. Beagle can also be used in conjunction with PRESTO, a program for fast and flexible permutation testing. PRESTO can compute empirical distributions of order statistics, analyze stratified data, and determine significance levels for one-stage and two-stage genetic association studies. BEAGLE is written in Java and runs on any computing platform with a Java version 1.6 interpreter (e.g. Windows, Unix, Linux, Solaris, Mac).

Proper citation: BEAGLE (RRID:SCR_001789) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/nondetects.html

Software R package to model and impute non-detects in results of qPCR experiments.Used to directly model non-detects as missing data.

Proper citation: nondetects (RRID:SCR_001702) Copy   

•   Source: SciCrunch Registry

https://www.apbenson.com/cyrillic-downloads

Software application for pedigree drawing with fully integrated risk analysis and support for industry standard databases (MS Access and Corel Paradox). It is designed for genetic counselors and others who work with patients. Cyrillic 2 draws pedigrees, works with genetic marker data, lets you do haplotyping and allows exports to a range of linkage analysis packages.

Proper citation: CYRILLIC (RRID:SCR_001823) Copy   

•   Source: SciCrunch Registry

http://clip.med.yale.edu/presto/

Software toolkit for processing raw reads from high-throughput sequencing of lymphocyte repertoires.

Proper citation: pRESTO (RRID:SCR_001782) Copy   

•   Source: SciCrunch Registry

https://omictools.com/prolinks-tool

THIS RESOURCE IS NO LONGER IN SERVICE, documented July 7, 2017. Collection of inference methods used to predict functional linkages between proteins. These methods include the Phylogenetic Profile method which uses the presence and absence of proteins across multiple genomes to detect functional linkages; the Gene Cluster method which uses genome proximity to predict functional linkage; Rosetta Stone which uses a gene fusion event in a second organism to infer functional relatedness; and the Gene Neighbor method which uses both gene proximity and phylogenetic distribution to infer linkage.

Proper citation: ProLinks Database of Functional Linkages (RRID:SCR_003185) Copy   

•   Source: SciCrunch Registry

http://collaborations.gis.a-star.edu.sg/~cmb6/TherMos/

Software used for estimating protein-DNA binding energies from in vivo binding profiles. It is a de novo motif discovery algorithm that exploits the information in transcription factor ChIP-seq or ChIP-exo datasets based on a more natural thermodynamic formalism., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: TherMos (RRID:SCR_002790) Copy   

•   Source: SciCrunch Registry

http://www.altanalyze.org/

Software application for microarry, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), it will assess alternative exon (known and novel) expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, it provides comprehensive methods for the analysis of other data (RMA summarization, batch-effect removal, QC, statistics, annotation, clustering, network creation, lineage characterization, alternative exon visualization, gene-set enrichement and more). AltAnalyze can be run through an intuitive graphical user interface or command-line and requires no advanced knowledge of bioinformatics programs or scripting. Alternative regulated exons can be subsequently visualized in the context of proteins, domains and microRNA binding sites with the Cytoscape Plugin DomainGraph.

Proper citation: AltAnalyze - Alternative Splicing Analysis Tool (RRID:SCR_002951) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/enviPick/

Software for sequential partitioning, clustering and peak detection of centroided LC-MS mass spectrometry data (.mzXML). Interactive result and raw data plot.

Proper citation: enviPick (RRID:SCR_003059) Copy   

•   Source: SciCrunch Registry

http://microarray.ym.edu.tw:8080/tools/module/set/index.jsp?mode=home

A Java tool to evaluate and visualize the sample discrimination abilities of gene expression signatures. This tool provides a filtration function for signature identification and lies between clinical analyses and class prediction (or feature selection) tools.

Proper citation: SET (RRID:SCR_003605) Copy   

•   Source: SciCrunch Registry

http://subread.sourceforge.net/

Software package for high-performance read alignment, quantification and mutation discovery.General purpose read aligner which can be used to map both genomic DNA-seq reads and RNA-seq reads. Subread aligner as fast, accurate and scalable read mapping by seed-and-vote.These programs were also implemented in Bioconductor R package Rsubread.

Proper citation: Subread (RRID:SCR_009803) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/

Software tool to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files for directional, non-directional or paired-end sequencing. Wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for Reduced Representation Bisulfite Sequencing data.

Proper citation: Trim Galore (RRID:SCR_011847) Copy   

•   Source: SciCrunch Registry

https://omictools.com/tiltpicker-tool

Software tool to facilitate particle selection in single particle electron microscopy. An interactive graphical interface application designed to streamline the selection of particle pairs from tilted-pair datasets. Designed to work with existing software tools for image processing.

Proper citation: TiltPicker (RRID:SCR_016674) Copy   

•   Source: SciCrunch Registry

https://chlorobox.mpimp-golm.mpg.de/geseq.html

Software tool for rapid and accurate annotation of organelle genomes, in particular chloroplast genomes.

Proper citation: GeSeq (RRID:SCR_017336) Copy   

•   Source: SciCrunch Registry

https://github.com/wdecoster/nanofilt

Software tool written in Python to perform its filtering based on mean read quality and GC content and read length. Used for filtering and trimming of long read sequencing data.

Proper citation: NanoFilt (RRID:SCR_016966) Copy   

•   Source: SciCrunch Registry

https://github.com/mandricigor/ScaffMatch

Software tool as scaffolding algorithm based on maximum weight matching able to produce high quality scaffolds from next generation sequencing data (reads and contigs). Able to handle reads with both short and long insert sizes.

Proper citation: ScaffMatch (RRID:SCR_017025) Copy   

•   Source: SciCrunch Registry

https://github.com/isovic/racon

Software tool as de novo genome assembly from long uncorrected reads. Used to correct raw contigs generated by rapid assembly methods which do not include consensus step. Supports data produced by Pacific Biosciences and Oxford Nanopore Technologies.

Proper citation: Racon (RRID:SCR_017642) Copy   

•   Source: SciCrunch Registry

https://github.com/TransDecoder/TransDecoder

Software tool to identify candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to genome using Tophat and Cufflinks.Starts from FASTA or GFF file. Can scan and retain open reading frames (ORFs) for homology to known proteins by using BlastP or Pfam search and incorporate results into obtained selection. Predictions can then be visualized by using genome browser such as IGV.

Proper citation: TransDecoder (RRID:SCR_017647) Copy   

•   Source: SciCrunch Registry