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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Nextflow Resource Report Resource Website 100+ mentions |
Nextflow (RRID:SCR_024135) | workflow software, software application, data processing software, software resource | Software workflow manager that enables development of portable and reproducible workflows.Supports deploying workflows on variety of execution platforms including local, HPC schedulers, AWS Batch, Google Cloud Life Sciences, and Kubernetes. Provides support to manage workflow dependencies through built-in support for Conda, Spack, Docker, Podman, Singularity, Modules, and more. | development of portable and reproducible workflows, deploying workflows, manage workflow dependencies, |
is listed by: Debian works with: NEXT-scASV |
PMID:28398311 | Free, Available for download, Freely available, | https://sources.debian.org/src/nextflow/, https://nextflow.io/ | SCR_024135 | nextflow | 2026-08-01 12:08:00 | 132 | |||||||
|
VADR Resource Report Resource Website 1+ mentions |
VADR (RRID:SCR_024377) | data processing software, data analysis software, software application, software resource | Software suite of tools for classifying and analyzing sequences homologous to set of reference models of viral genomes or gene families. | classifying and analyzing sequences, sequences homologous to set of reference models, viral genomes reference models, gene families reference models, | is listed by: Debian | PMID:35441162 | Free, Available for download, Freely available, | https://sources.debian.org/src/vadr/ | SCR_024377 | ushahidi | 2026-08-01 12:08:26 | 1 | |||||||
|
FISH Resource Report Resource Website 1+ mentions |
FISH (RRID:SCR_024378) | data processing software, data analysis software, software application, software resource | Software tool for identifying regions of common ancestry between genome maps. Used for identification and statistical evaluation of segmental homologies in comparative maps. | identifying regions of common ancestry, genome maps, identification and statistical evaluation, segmental homologies in comparative maps, | is listed by: Debian | PMID:12855440 | Free, Available for download, Freely available, | OMICS_11724 | https://sources.debian.org/src/unc-fish/ | SCR_024378 | 2026-08-01 12:08:26 | 1 | |||||||
|
TopHat-Recondition Resource Report Resource Website |
TopHat-Recondition (RRID:SCR_024383) | data processing software, software application, software resource | Software tool as post-processor for TopHat unmapped reads that restores read information in the proper format.Enables downstream software to process plethora of BAM files written by TopHat. | post-processor for TopHat unmapped reads, restore read information in the proper format, process plethora of BAM files written by TopHat, | is listed by: Debian | PMID:27142976 | Free, Available for download, Freely available, | https://sources.debian.org/src/tophat-recondition/ | SCR_024383 | 2026-08-01 12:08:01 | 0 | ||||||||
|
omegaMap Resource Report Resource Website 10+ mentions |
omegaMap (RRID:SCR_024143) | data processing software, data analysis software, software application, software resource | Software tool for detecting natural selection and recombination in DNA or RNA sequences. | detecting natural selection and recombination, DNA sequences, RNA sequences | is listed by: Debian | DOI:10.1534/genetics.105.044917 | Free, Available for download, Freely available, | OMICS_31719 | https://sources.debian.org/src/omegamap/ | SCR_024143 | omegamap | 2026-08-01 12:08:25 | 32 | ||||||
|
OpenEMR Resource Report Resource Website 1+ mentions |
OpenEMR (RRID:SCR_024144) | software resource, software application, data management software | Open source software for electronic health records and medical practice management solution. | electronic health records, medical practice management, | is listed by: Debian | Free, Available for download, Freely available, | https://github.com/openemr/openemr | https://sources.debian.org/src/openemr/ | SCR_024144 | openemr | 2026-08-01 12:08:15 | 1 | |||||||
|
Tombo Resource Report Resource Website 10+ mentions |
Tombo (RRID:SCR_024388) | data processing software, data analysis software, software application, software resource | Software suite of tools for identification of modified nucleotides from nanopore sequencing data.Used also for analysis and visualization of raw nanopore signal. | identification of modified nucleotides, nanopore sequencing data, analysis and visualization of raw nanopore signal, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/tombo/ | SCR_024388 | ont-tombo | 2026-08-01 12:08:01 | 14 | ||||||||
|
NW-align Resource Report Resource Website |
NW-align (RRID:SCR_024138) | image analysis software, data access protocol, alignment software, software application, data processing software, software resource, web service | Software tool as alignment program for protein sequence-to-sequence alignments based on the standard Needleman-Wunsch dynamic programming algorithm. | protein sequence-to-sequence alignments, standard Needleman-Wunsch dynamic programming algorithm, | is listed by: Debian | Free, Freely available, | https://sources.debian.org/src/nw-align/ | SCR_024138 | nw-align | 2026-08-01 12:08:15 | 0 | ||||||||
|
MicrobeGPS Resource Report Resource Website |
MicrobeGPS (RRID:SCR_024112) | data processing software, data analysis software, software application, software resource | Software tool for analysis of metagenomic sequencing data.Used to profile composition of metagenomic communities. Calculates quality metrics for estimated candidates and allows the user to identify false candidates. | metagenomic sequencing data analysis, profile composition of metagenomic communities, identify false candidates, | is listed by: Debian | PMID:25643362 | Free, Available for download, Freely available, | OMICS_17085 | https://sources.debian.org/src/microbegps/ | SCR_024112 | microbegps | 2026-08-01 12:08:14 | 0 | ||||||
|
surankco Resource Report Resource Website 1+ mentions |
surankco (RRID:SCR_024355) | software resource, software application, simulation software | Machine learning based software to score and rank contigs from de novo assemblies of next generation sequencing data. It trains with alignments of contigs with known reference genomes and predicts scores and ranking for contigs which have no related reference genome yet. | score and rank contigs, de novo assemblies of next generation sequencing data, | is listed by: Debian | PMID:26224355 | Free, Available for download, Freely available, | OMICS_09480 | https://sources.debian.org/src/surankco/ | SCR_024355 | 2026-08-01 12:08:26 | 1 | |||||||
|
pyscanfcs Resource Report Resource Website |
pyscanfcs (RRID:SCR_024190) | data processing software, data analysis software, software application, software resource | Software application for perpendicular line scanning fluorescence correlation spectroscopy. | perpendicular line scanning, fluorescence correlation spectroscopy, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_21694 | https://sources.debian.org/src/pyscanfcs/ | SCR_024190 | 2026-08-01 12:08:26 | 0 | ||||||||
|
pyranges Resource Report Resource Website 1+ mentions |
pyranges (RRID:SCR_024191) | data processing software, data analysis software, software application, software resource | Software application for efficient comparison of genomic intervals in Python. | comparison of genomic intervals, Python | is listed by: Debian | PMID:31373614 | Free, Available for download, Freely available, | https://sources.debian.org/src/python3-pyranges/ | SCR_024191 | 2026-08-01 12:08:15 | 4 | ||||||||
|
Chado Resource Report Resource Website 1+ mentions |
Chado (RRID:SCR_024073) | software resource, software application, data management software | Relational database schema that underlies many GMOD installations. It is capable of representing many of the general classes of data frequently encountered in modern biology such as sequence, sequence comparisons, phenotypes, genotypes, ontologies, publications, and phylogeny. It has been designed to handle complex representations of biological knowledge and should be considered one of the most sophisticated relational schemas currently available in molecular biology. The price of this capability is that the new user must spend some time becoming familiar with its fundamentals. | database schema, GMOD installations, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libchado-perl/ | SCR_024073 | libchado-perl | 2026-08-01 12:07:59 | 1 | ||||||||
|
yaha Resource Report Resource Website |
yaha (RRID:SCR_024365) | aligment software | Software tool as fast and flexible long read alignment with optimal breakpoint detection. | fast and flexible long-read alignment, optimal breakpoint detection, | is listed by: Debian | PMID:22829624 | Free, Available for download, Freely available, | OMICS_04675 | https://sources.debian.org/src/yaha/ | SCR_024365 | YAHA | 2026-08-01 12:08:01 | 0 | ||||||
|
Mustang Resource Report Resource Website 1+ mentions |
Mustang (RRID:SCR_024126) | image analysis software, alignment software, software application, software resource, data processing software | Software tool for structural alignment of multiple protein structures. Used to produce sequence alignment. Reports multiple sequence alignment and corresponding superposition of structures. | structural alignment, multiple protein structures, produce sequence alignment, | is listed by: Debian | PMID:16736488 | Free, Available for download, Freely available, | OMICS_03642 | https://sources.debian.org/src/mustang/ | SCR_024126 | mustang, MUltiple (protein) STructural AligNment alGorithm, MUSTANG | 2026-08-01 12:08:25 | 4 | ||||||
|
zAlign Resource Report Resource Website |
zAlign (RRID:SCR_024360) | aligment software | Software tool as local sequence aligner intended for use with large biological DNA sequences, with more than 1 Millions of base pairs. | sequence aligner, large biological DNA sequences, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_21299 | https://sources.debian.org/src/zalign/ | SCR_024360 | zalign | 2026-08-01 12:08:16 | 0 | |||||||
|
mlgt Resource Report Resource Website |
mlgt (RRID:SCR_001211) | mlgt | software resource, software application, data processing software | Software for processing and analysis of high throughput (Roche 454) sequences generated from multiple loci and multiple biological samples. Sequences are assigned to their locus and sample of origin, aligned and trimmed. Where possible, genotypes are called and variants mapped to known alleles. | roche, windows, os x, genotype, variant, allele, high throughput sequencing, locus, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Manchester; Manchester; United Kingdom |
THIS RESOURCE IS NO LONGER IN SERVICE | BioTools:mlgt, OMICS_02131, biotools:mlgt | https://bio.tools/mlgt, https://bio.tools/mlgt, https://bio.tools/mlgt | SCR_001211 | Multi-Locus Geno-Typing, mlgt: Multi-Locus Geno-Typing | 2026-08-01 12:08:17 | 0 | ||||||
|
SOAP Resource Report Resource Website 100+ mentions |
SOAP (RRID:SCR_000689) | SOAP, | software resource, software application, data processing software | Software package that provides full solution to next generation sequencing data analysis consisting of an alignment tool (SOAPaligner/soap2), a re-sequencing consensus sequence builder (SOAPsnp), an indel finder ( SOAPindel ), a structural variation scanner ( SOAPsv ), a de novo short reads assembler ( SOAPdenovo ), and a GPU-accelerated alignment tool for aligning short reads with a reference sequence. (SOAP3/GPU)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, next generation sequencing, alignment, short read, bio.tools |
lists: SOAPfusion lists: SOAPfuse lists: SOAPnuke lists: GapCloser is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: BGI; Shenzhen; China is parent organization of: SOAP3 is parent organization of: SOAPaligner/soap2 |
PMID:18227114 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154652, biotools:soap | https://bio.tools/soap | SCR_000689 | SOAP: short oligonucleotide alignment program, Short Oligonucleotide Analysis Package | 2026-08-01 12:08:20 | 402 | |||||
|
IQ TREE Resource Report Resource Website 100+ mentions |
IQ TREE (RRID:SCR_021163) | data processing software, data analysis software, software application, software resource | Software tool for phylogenomic inference. | phylogenomic inference, tree of life, data analysis |
is listed by: Debian is listed by: OMICtools |
Austrian Science Fund FWF ; University of Vienna |
Free, Available for download, Freely available | OMICS_11543 | https://sources.debian.org/src/iqtree/ | SCR_021163 | 2026-08-01 12:07:13 | 350 | |||||||
|
QIIME2 Resource Report Resource Website 1000+ mentions |
QIIME2 (RRID:SCR_021258) | data analysis software, software application, software resource, sequence analysis software, data processing software | Software tool as next generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.Enables researchers to start analysis with raw DNA sequence data and finish with publication quality figures and statistical results. Used to analyze and interpret nucleic acid sequence data from fungal, viral, bacterial, and archaeal communities. | Nucleic acid sequence data, nucleic acid sequence, fungal data, viral data, bacterial data, archaeal data, data analysis |
is used by: Tourmaline is used by: RiboSnake is listed by: Debian is listed by: OMICtools |
Free, Available for download, Freely available | https://github.com/qiime2/qiime2, https://sources.debian.org/src/q2-sample-classifier/ | SCR_021258 | Quantitative Insights Into Microbial Ecology 2 | 2026-08-01 12:07:15 | 1232 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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