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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SimRare Resource Report Resource Website 1+ mentions |
SimRare (RRID:SCR_005226) | SimRare | software resource | A stand-alone executable software with user-friendly graphical interface implemented in Python/C++ for rare variant association studies. It is designed as a unified simulation framework to provide an unbiased and easy manner to evaluate association methods, including novel methods, under a broad range of choice of biological contexts. It consists of three modules, variant data simulator, genotype/phenotype generator and association method evaluator. SimRare generates variant data for gene regions using forward-time simulation which incorporates realistic population demographic and evolutionary scenarios. For phenotype data it is capable of generating both case-control and quantitative traits. The phenotypic effects of variants can be detrimental, protective or non-causal. SimRare has a graphical user interface which allows for easy entry of genetic and phenotypic parameters. Simulated data can be written into external files in a standard format. For novel association method implemented in R it can be imported into SimRare, which has been equipped built in functions to evaluate performance of new method and visually compare it with currently available ones in an unbiased manner. | statistical genetics, simulation framework, gui, association test, sequencing, rare variant, python, c++, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Google Code has parent organization: Baylor University; Texas; USA |
PMID:22914216 | Acknowledgement requested, GNU General Public License, v3 | OMICS_00257, biotools:simrare | https://bio.tools/simrare | SCR_005226 | SimRare - A program to generate and analyze sequence-based data for rare variant association studies of quantitative and qualitative traits | 2026-02-14 02:00:51 | 2 | |||||
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Breakpointer Resource Report Resource Website 1+ mentions |
Breakpointer (RRID:SCR_005254) | Breakpointer | software resource | A fast tool for locating sequence breakpoints from the alignment of single end reads (SE) produced by next generation sequencing (NGS). It adopts a heuristic method in searching for local mapping signatures created by insertion/deletions (indels) or more complex structural variants(SVs). With current NGS single-end sequencing data, the output regions by Breakpoint mainly contain the approximate breakpoints of indels and a limited number of large SVs. Notably, Breakpointer can uncover breakpoints of insertions which are longer than the read length. Breakpointer also can find breakpoints of many variants located in repetitive regions. The regions can be used not only as a extra support for SV predictions by other tools (such as by split-read method), but also can serve as a database for searching variants which might be missed by other tools. Breakpointer is a command line tool that runs under linux system. Breakpointer takes advanage of two local mapping features of single-end reads as a consequence of indel/SVs: 1) non-uniform read distribution (depth skewness) and 2) misalignments at the boundaries of indel/SVs. These features are summarized as breakpoint signature. Breakpointer proceeds in three stages in capturing this signature. It is implemented in C++ and perl. Input is the file or files containing alignments of single-end reads against a reference genome (in .BAM format). Output is the predicted regions containing potential breakpoints of SVs (in .GFF format). To be able to read in .BAM files, Breakpointer requires bamtools API, which users should install beforehand. | next-generation sequencing, c++, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Max Planck Institute for Molecular Genetics; Berlin; Germany |
GNU General Public License | biotools:breakpointer, OMICS_00308 | https://bio.tools/breakpointer | SCR_005254 | 2026-02-14 02:01:04 | 9 | |||||||
|
G-Mo.R-Se Resource Report Resource Website 1+ mentions |
G-Mo.R-Se (RRID:SCR_005273) | G-Mo.R-Se | software resource | Software aimed at using RNA-Seq short reads to build de novo gene models. First, candidate exons are built directly from the positions of the reads mapped on the genome (without any ab initio assembly of the reads), and all the possible splice junctions between those exons are tested against unmapped reads : the testing of junctions is directed by the information available in the RNA-Seq dataset rather than a priori knowledge about the genome. Exons can thus be chained into stranded gene models. | bio.tools, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_01259, biotools:g-mo.r-se, biotools:gmorse | https://bio.tools/g-mo.r-se https://bio.tools/gmorse |
SCR_005273 | Gene MOdeling using RNA-Seq, G-Mo.R-Se: Gene MOdeling using RNA-Seq | 2026-02-14 02:01:05 | 1 | |||||||
|
inGAP Resource Report Resource Website 10+ mentions |
inGAP (RRID:SCR_005261) | inGAP | software resource | Software mining pipeline guided by a Bayesian principle to detect single nucleotide polymorphisms, insertion and deletions by comparing high-throughput pyrosequencing reads with a reference genome of related organisms. This pipeline is extended to identify and visualize large-size structural variations, including insertions, deletions, inversions and translocations. | structural variation, genome, next-generation sequence, genome analysis, alignment, single nucleotide polymorphism, insertion, deletion, indel, inversion, translocation, windows, linux, macos/x, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Fudan University; Shanghai; China has parent organization: Chinese Academy of Sciences; Beijing; China |
OMICS_00319, biotools:ingap | https://bio.tools/ingap | SCR_005261 | inGAP-sv, inGAP-sv: structural variation detection and visualization, integrative next-generation genome analysis pipeline | 2026-02-14 02:00:51 | 29 | |||||||
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PEMer Resource Report Resource Website 1+ mentions |
PEMer (RRID:SCR_005263) | software resource | Software package as computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Package is composed of three modules, PEMer workflow, SV-Simulation and BreakDB. PEMer workflow is a sensitive software for detecting SVs from paired-end sequence reads. SV-Simulation randomly introduces SVs into a given genome and generates simulated paired-end reads from novel genome. | structural variation, genome, next-generation sequencing, bio.tools, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: BreakDB has parent organization: European Molecular Biology Laboratory |
PMID:19236709 | biotools:pemer, OMICS_00320 | https://bio.tools/pemer https://bio.tools/pemer |
SCR_005263 | Paired-End Mapper | 2026-02-14 02:01:04 | 7 | |||||||
|
phantompeakqualtools Resource Report Resource Website 50+ mentions |
phantompeakqualtools (RRID:SCR_005331) | phantompeakqualtools | software resource | Software package that computes quick but highly informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays. | chip-seq, dnase-seq, faire-seq, mnase-seq, dataquality, enrichment, phantompeak, cross-correlation, spppeakcaller, chipseq, dnaseseq, fairseq, mnaseseq, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
MIT License | biotools:phantompeakqualtools, OMICS_00431 | https://bio.tools/phantompeakqualtools | SCR_005331 | phantompeakqualtools - Computes quick but highly informative enrichment and quality measures and fragment lengths for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data | 2026-02-14 02:00:52 | 86 | ||||||
|
WHAM Resource Report Resource Website 100+ mentions |
WHAM (RRID:SCR_005497) | WHAM | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. High-throughput sequence alignment tool that aligns short DNA sequences (reads) to the whole human genome at a rate of over 1500 million 60bps reads per hour, which is one to two orders of magnitudes faster than the leading state-of-the-art techniques. Feature list for the current version (v 0.1.5) of WHAM: * Supports paired-end reads * Supports up to 5 errores * Supports alignments with gaps * Supports quality scores for filtering invalid alignments, and sorting valid alignments * finds ALL valid alignments * Supports multi-threading * Supports rich reporting modes * Supports SAM format output | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
Facebook ; NSF IIS-1110948 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00697, biotools:wham | https://bio.tools/wham https://sources.debian.org/src/wham-align/ |
SCR_005497 | Wisconsin?s High-throughput Alignment Method | 2026-02-14 02:01:07 | 345 | |||||
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SeqMap Resource Report Resource Website 50+ mentions |
SeqMap (RRID:SCR_005495) | SeqMap | software resource | A software tool for mapping large amount of oligonucleotide to the genome. It is designed for finding all the places in a genome where an oligonucleotide could potentially come from. SeqMap can efficiently map as many as dozens of millions of short sequences to a genome of several billions of nucleotides. While doing the mapping, several mutations as well as insertions / deletions of the nucleotide bases in the sequences can be tolerated and furthermore detected. Various input and output formats are supported, as well as many command line options for tuning almost every steps in the mapping process. A typical mapping can be done in a few hours on an ordinary PC. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Michigan; Ann Arbor; USA |
PMID:18697769 | Free, Non-commercial, Commercial use requires permission | biotools:seqmap, OMICS_00684 | https://bio.tools/seqmap | SCR_005495 | SeqMap - A Tool For Mapping Millions Of Short Sequences To The Genome | 2026-02-14 02:01:08 | 95 | |||||
|
Jellyfish Resource Report Resource Website 1000+ mentions |
Jellyfish (RRID:SCR_005491) | Jellyfish | software resource | A software tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers quickly by using an efficient encoding of a hash table and by exploiting the compare-and-swap CPU instruction to increase parallelism. Jellyfish is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the jellyfish dump command., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | c++, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Maryland; Maryland; USA |
PMID:21217122 DOI:10.1093/bioinformatics/btr011 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:jellyfish, OMICS_01056 | https://bio.tools/jellyfish https://sources.debian.org/src/jellyfish1/ |
SCR_005491 | Jellyfish mer counter | 2026-02-14 02:00:54 | 1130 | |||||
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mrFAST Resource Report Resource Website 10+ mentions |
mrFAST (RRID:SCR_005487) | mrFAST | software resource | Software designed to map short reads generated with the Illumina platform to reference genome assemblies; in a fast and memory-efficient mannerl. Currently Supported Features: * Output in SAM format * Indels up to 8 bp (4 bp deletions and 4 bp insertions) * Paired-end mapping ** Discordant option to generate mapping file ready for VariationHunter to detect structural variants. * One end anchored (OEA) map locations for novel sequence insertion detection with NovelSeq * Matepair library mapping (long inserts with RF orientation). Planned Features: * Multithreading | next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: SPLITREAD has parent organization: SourceForge |
PMID:19718026 | biotools:mrfast, OMICS_00671 | https://bio.tools/mrfast | SCR_005487 | mrFAST - Micro Read Fast Alignment Search Tool, Micro Read Fast Alignment Search Tool | 2026-02-14 02:00:54 | 16 | ||||||
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GNUMAP Resource Report Resource Website 1+ mentions |
GNUMAP (RRID:SCR_005482) | GNUMAP | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 3rd,2023. A software program designed to accurately map sequence data obtained from next-generation sequencing machines (specifically that of Solexa/Illumina) back to a genome of any size. By using the posterior probability of mapping a given read to a specific genomic loation, we are able to account for repetitive reads by distributing them across several regions in the genome. In addition, the output of the program is created in such a way that it can be easily viewed through other free and readily- available programs. Several benchmark data sets were created with spiked-in duplicate regions, and GNUMAP was able to more accurately account for these duplicate regions. | next-generation sequencing, genome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Brigham Young University; Utah; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00664, biotools:gnumap | https://bio.tools/gnumap | SCR_005482 | Genomic Next-generation Universal MAPper | 2026-02-14 02:00:54 | 7 | ||||||
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SAMStat Resource Report Resource Website 10+ mentions |
SAMStat (RRID:SCR_005432) | SAMStat | software resource | C software program for displaying sequence statistics for next generation sequencing. Works with large fasta, fastq and SAM/BAM files. | sequence statistic, c, next generation sequencing, fasta file, fastq file, sam file, bam file, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: RIKEN Yokohama Institute; Kanagawa; Japan |
PMID:21088025 | Acknowledgement requested | biotools:samstat, OMICS_01073 | https://bio.tools/samstat | SCR_005432 | 2026-02-14 02:00:53 | 38 | ||||||
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MethylViewer Resource Report Resource Website 1+ mentions |
MethylViewer (RRID:SCR_005448) | MethylViewer | software resource | A simple integrated software tool for handling MAP (methyltransferase accessibility protocol) and MAP-IT (MAP individual templates) footprinting projects. It can process sequence data (*.txt, *.ab1 and *.scf) derived from the use of up to four different DNA methyltransferases. | primer design, bisulfite sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Leeds; West Yorkshire; United Kingdom |
PMID:20959287 | OMICS_00608, biotools:methylviewer | https://bio.tools/methylviewer | SCR_005448 | 2026-02-14 02:00:55 | 2 | |||||||
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Bis-SNP Resource Report Resource Website 50+ mentions |
Bis-SNP (RRID:SCR_005439) | Bis-SNP | software resource | A software package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping and accurate DNA methylation calling in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq, RRBS and any other bisulfite treated sequencing) with Illumina directional library protocol. It contains the following key features: * Call and summarize methylation of any cytosine context provided (CpG, CHH, CHG, GCH et.al.); * Work for single end and paired-end data; * Accurtae variant detection. Enable base quality recalibration and indel calling in bisulfite sequencing; * Based on Java map-reduce framework, allow multi-thread computing. Cross-platform; * Allow multiple output format, detailed VCF files, CpG haplotype reads file for mono-allelic methylation analysis, simplified bedGraph, wig and bed format for visualization in UCSC genome broswer and IGV browser. BisSNP uses bayesian inference with locus specific methylation probabilities and bisulfite conversion rate of different cytosine context(not only CpG, CHH, CHG in Bisulfite-seq, but also GCH et.al. in other bisulfite treated sequencing) to determine genotypes and methylation levels simultaneously., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Southern California; Los Angeles; USA |
PMID:22784381 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:bis-snp, OMICS_00591 | https://bio.tools/bis-snp | SCR_005439 | Bis-SNP - A bisulfite space genotyper & methylation caller, Bis-SNP - A bisulfite space genotyper and methylation caller | 2026-02-14 02:00:54 | 50 | |||||
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DistMap Resource Report Resource Website 10+ mentions |
DistMap (RRID:SCR_005473) | DistMap | software resource | A user-friendly software pipeline designed to map short reads in a MapReduce framework on a local Hadoop cluster. It is designed to be easily implemented by researchers who do not have expert knowledge of bioinformatics. As it does not have any dependencies, it provides full flexibility and control to the user. The user can use any version of a compatible mapper and any reference genome assembly. There is no need to maintain the mapper, reference or DistMap source code on each of the slaves (nodes) in the Hadoop cluster, making maintenance extremely easy. | mapreduce/hadoop, command line, hadoop cluster, next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Veterinary Medicine Vienna; Vienna; Austria has parent organization: Google Code |
PMID:24009693 | GNU General Public License, v3 | OMICS_00660, biotools:distmap | https://bio.tools/distmap | SCR_005473 | 2026-02-14 02:01:06 | 23 | ||||||
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Stampy Resource Report Resource Website 100+ mentions |
Stampy (RRID:SCR_005504) | Stampy | software resource | A software package for the mapping of short reads from illumina sequencing machines onto a reference genome. It''s recommended for most workflows, including those for genomic resequencing, RNA-Seq and Chip-seq. Stampy excels in the mapping of reads containing that contain sequence variation relative to the reference, in particular for those containing insertions or deletions. It can map reads from a highly divergent species to a reference genome for instance. Stampy achieves high sensitivity and speed by using a fast hashing algorithm and a detailed statistical model. Stampy has the following features: * Maps single, paired-end and mate pair Illumina reads to a reference genome * Fast: about 20 Gbase per hour in hybrid mode (using BWA) * Low memory footprint: 2.7 Gb shared memory for a 3Gbase genome * High sensitivity for indels and divergent reads, up to 10-15% * Low mapping bias for reads with SNPs * Well calibrated mapping quality scores * Input: Fastq and Fasta; gzipped or plain * Output: SAM, Maq''s map file * Optionally calculates per-base alignment posteriors * Optionally processes part of the input * Handles reads of up to 4500 bases | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Wellcome Trust Centre for Human Genetics |
PMID:20980556 | OMICS_00691, biotools:stampy | https://bio.tools/stampy | SCR_005504 | 2026-02-14 02:01:07 | 182 | |||||||
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NGSView Resource Report Resource Website 1+ mentions |
NGSView (RRID:SCR_005637) | NGSView | software resource | A generally applicable, flexible and extensible next-generation sequence alignment editor. The software allows for visualization and manipulation of millions of sequences simultaneously on a desktop computer, through a graphical interface. | next-generation sequence, alignment, edit, visualization, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
Acknowledgement requested | biotools:ngsview, OMICS_00891 | https://bio.tools/ngsview | SCR_005637 | 2026-02-14 02:00:58 | 2 | |||||||
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HiCUP Resource Report Resource Website 100+ mentions |
HiCUP (RRID:SCR_005569) | HiCUP | software resource | A tool for mapping and performing quality control on Hi-C data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Babraham Institute |
OMICS_00523, biotools:hicup | https://bio.tools/hicup | SCR_005569 | Hi-C User Pipeline | 2026-02-14 02:01:09 | 273 | |||||||
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RUM Resource Report Resource Website 1+ mentions |
RUM (RRID:SCR_008818) | RUM | software resource | An alignment, junction calling, and feature quantification pipeline specifically designed for Illumina RNA-Seq data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
OMICS_01249, biotools:rum | https://bio.tools/rum https://github.com/itmat/rum/wiki |
SCR_008818 | Rna seq Unified Mapper | 2026-02-14 02:01:48 | 7 | |||||||
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QuasiRecomb Resource Report Resource Website 10+ mentions |
QuasiRecomb (RRID:SCR_008812) | QuasiRecomb | software resource | A jumping hidden Markov model that describes the generation of the viral quasispecies and a method to infer its parameters by analysing next generation sequencing data. | haplotype, next-generation sequencing, virus, parameter, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23383997 | OMICS_00229, biotools:quasirecomb | https://bio.tools/quasirecomb | SCR_008812 | QuasiRecomb - Probabilistic inference of viral Quasispecies | 2026-02-14 02:01:45 | 32 |
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