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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
BioLemmatizer Resource Report Resource Website 1+ mentions |
BioLemmatizer (RRID:SCR_000117) | software resource | A domain-specific lemmatization software tool for the morphological analysis of biomedical literature. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22464129 | Free, Available for download, Freely available | OMICS_04827 | https://sourceforge.net/projects/biolemmatizer/ | SCR_000117 | 2026-02-14 01:59:37 | 2 | |||||||
|
SOAPfuse Resource Report Resource Website 1+ mentions |
SOAPfuse (RRID:SCR_000078) | SOAPfuse | software resource | 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 . | software, resource, open license, DNA sequencing, genome, transcripts, RNA, oligonucleotide |
is listed by: OMICtools is listed by: SourceForge is listed by: SOAP |
PMID:23409703 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01357 | SCR_000078 | 2026-02-14 01:59:36 | 7 | |||||||
|
CNV Workshop Resource Report Resource Website 1+ mentions |
CNV Workshop (RRID:SCR_012635) | CNV Workshop | software resource | Software for a web-enabled platform for analyzing genome variation such as copy number variation (CNV). |
is listed by: OMICtools has parent organization: SourceForge |
GNU Affero General Public License | OMICS_00715 | SCR_012635 | 2026-02-14 02:02:15 | 1 | |||||||||
|
Krona Resource Report Resource Website 50+ mentions |
Krona (RRID:SCR_012785) | Krona | software resource | Software that allows hierarchical data to be explored with zoomable pie charts. | bio.tools |
is listed by: bio.tools has parent organization: SourceForge |
PMID:21961884 | OMICS_01498, biotools:krona | https://bio.tools/krona | SCR_012785 | Krona - Hierarchical data browser | 2026-02-14 02:02:23 | 89 | ||||||
|
Acacia Resource Report Resource Website 100+ mentions |
Acacia (RRID:SCR_012896) | Acacia | software resource | Accurate error-correction of amplicon pyrosequences. |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
DOI:10.1038/nmeth.1990 | OMICS_01116 | https://sources.debian.org/src/acacia/ | SCR_012896 | 2026-02-14 02:02:48 | 106 | ||||||||
|
IBDLD Resource Report Resource Website 10+ mentions |
IBDLD (RRID:SCR_013043) | IBDLD | software resource | A C++ software program for multipoint IBD estimation based on high density SNP genotype data. | c++ |
is listed by: OMICtools has parent organization: SourceForge |
PMID:21769932 | Free | OMICS_00204 | SCR_013043 | 2026-02-14 02:02:49 | 14 | |||||||
|
SolSNP Resource Report Resource Website 1+ mentions |
SolSNP (RRID:SCR_013045) | SolSNP | software resource | A Java-based DNA variant calling tool for Next-Generation Sequencing alignment data. |
is listed by: OMICtools has parent organization: SourceForge |
MIT License | OMICS_00079 | SCR_013045 | 2026-02-14 02:02:45 | 7 | |||||||||
|
HATS Resource Report Resource Website 10+ mentions |
HATS (RRID:SCR_013044) | HATS | software resource | A software tool that calls the amplified alleles, and thus amplified haplotype, in copy number aberration regions in next generation sequencing tumor data. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00200 | SCR_013044 | Haplotype Amplification in Tumor Sequences | 2026-02-14 02:02:21 | 37 | |||||||||
|
ChIPOTle Peak Finder Resource Report Resource Website |
ChIPOTle Peak Finder (RRID:SCR_012991) | ChIPOTle Peak Finder | software resource | A peak-finding algorithm used to analyze ChIP-chip microarray data. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00803 | SCR_012991 | 2026-02-14 02:02:45 | 0 | ||||||||||
|
Trinity Resource Report Resource Website 5000+ mentions |
Trinity (RRID:SCR_013048) | Trinity | software resource | Software for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Broad Institute has parent organization: Hebrew University of Jerusalem; Jerusalem; Israel |
DOI:10.1038/nbt.1883 | biotools:trinity, OMICS_01327 | https://bio.tools/trinity https://sources.debian.org/src/trinityrnaseq/ |
SCR_013048 | 2026-02-14 02:02:49 | 9576 | |||||||
|
NGSpeAnalysis Resource Report Resource Website |
NGSpeAnalysis (RRID:SCR_013040) | NGSpeAnalysis | software resource | A pipeline using open-source tools which can implement a set of pair ended Next-generation sequencing analysis, include short reads alignment, high-quality variation genotype calling and variants annotation. |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v2 | OMICS_00291 | SCR_013040 | 2026-02-14 02:02:21 | 0 | |||||||||
|
LoFreq Resource Report Resource Website 500+ mentions |
LoFreq (RRID:SCR_013054) | LoFreq | software resource | A fast and sensitive variant-caller for inferring single-nucleotide variants (SNVs) from high-throughput sequencing data. |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:23066108 DOI:10.1093/nar/gks918 |
Free, Freely available | OMICS_00063 | https://sources.debian.org/src/lofreq/ | SCR_013054 | LoFreq - Sensitive variant-calling from sequencing data | 2026-02-14 02:02:21 | 523 | ||||||
|
GENE-counter Resource Report Resource Website 1+ mentions |
GENE-counter (RRID:SCR_013056) | GENE-counter | software resource | A computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression of eukaryotes, prokaryotes, as well as organisms with no available genome reference sequence. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21998647 | OMICS_01404, biotools:gene-counter | https://bio.tools/gene-counter | SCR_013056 | 2026-02-14 02:02:26 | 7 | |||||||
|
RNA CoMPASS Resource Report Resource Website |
RNA CoMPASS (RRID:SCR_013058) | RNA CoMPASS | software resource | A web-based GUI distributed computational pipeline, provides all-in-one functionality including human transcriptome quantification and the typical endogenous RNA-Sequencing analysis along with the investigation of exogenous sequences. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01410 | SCR_013058 | 2026-02-14 02:02:49 | 0 | ||||||||||
|
SNPTools Resource Report Resource Website 10+ mentions |
SNPTools (RRID:SCR_013052) | SNPTools | software resource | A suite of software tools that enables integrative SNP analysis in next generation sequencing data with large cohorts. | c++ |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00075 | SCR_013052 | 2026-02-14 02:02:26 | 19 | |||||||||
|
Swift Resource Report Resource Website 50+ mentions |
Swift (RRID:SCR_013018) | Swift | software resource | An open source package for primary data analysis on next-gen sequence data from images to basecalls. Currently Swift is targeted toward Solexa/Illumina sequencing, but is designed to be platform agnostic. |
is listed by: OMICtools has parent organization: SourceForge |
Open unspecified license | OMICS_01157 | SCR_013018 | 2026-02-14 02:02:49 | 74 | |||||||||
|
CloudAligner Resource Report Resource Website 1+ mentions |
CloudAligner (RRID:SCR_012962) | CloudAligner | software resource | A map/reduce based application for mapping short reads generated by the next-generation sequencing machines. | matlab, mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21645377 | GNU General Public License, v3 | OMICS_00656, biotools:cloudaligner | https://bio.tools/cloudaligner | SCR_012962 | 2026-02-14 02:02:19 | 4 | ||||||
|
TraceTuner Resource Report Resource Website 10+ mentions |
TraceTuner (RRID:SCR_013019) | TraceTuner | software resource | Software tool for base and quality calling of trace files from DNA sequencing instruments. |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
Free | OMICS_01158 | https://sources.debian.org/src/tracetuner/ | SCR_013019 | TraceTuner - DNA sequencing quality values base calling and trace processing | 2026-02-14 02:02:20 | 13 | |||||||
|
seqMINER Resource Report Resource Website 100+ mentions |
seqMINER (RRID:SCR_013020) | seqMINER | software resource | Software for a genome wide mapping data interpretation platform for NGS (ChIPSeq). | java, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21177645 | GNU General Public License, v3 | biotools:seqminer, OMICS_00460 | https://bio.tools/seqminer | SCR_013020 | 2026-02-14 02:02:45 | 187 | ||||||
|
MIREAP Resource Report Resource Website 100+ mentions |
MIREAP (RRID:SCR_013025) | MIREAP | software resource | A software tool which can be used to identify both known and novel microRNAs from small RNA libraries deeply sequenced by Solexa/454/Solid technology. |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v2 | OMICS_00376 | SCR_013025 | 2026-02-14 02:02:20 | 371 |
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