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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
ChimeraSlayer Resource Report Resource Website 100+ mentions |
ChimeraSlayer (RRID:SCR_013283) | ChimeraSlayer | software resource | A chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500 bp). | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
OMICS_01113, biotools:chimeraslayer | https://bio.tools/chimeraslayer | SCR_013283 | 2026-07-25 12:07:47 | 319 | ||||||||
|
Telescoper Resource Report Resource Website |
Telescoper (RRID:SCR_013206) | Telescoper | software resource | An algorithm that iteratively extends long paths through a series of read-overlap graphs and evaluates them based on a statistical framework. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:22962446 | biotools:telescoper, OMICS_00036 | https://bio.tools/telescoper | SCR_013206 | Telescoper - De novo assembly algorithm | 2026-07-25 12:07:49 | 0 | ||||||
|
palfinder Resource Report Resource Website 1+ mentions |
palfinder (RRID:SCR_013174) | palfinder | software resource | A perl script that finds microsatellite repeat elements directly from raw 454 or Illumina paired-end sequencing reads. | pacific biosciences |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00111 | SCR_013174 | 2026-07-25 12:07:49 | 6 | |||||||||
|
IsoLasso Resource Report Resource Website 1+ mentions |
IsoLasso (RRID:SCR_013176) | IsoLasso | software resource | An algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_01320, biotools:isolasso | https://bio.tools/isolasso | SCR_013176 | 2026-07-25 12:07:46 | 3 | ||||||||
|
sam comp Resource Report Resource Website |
sam comp (RRID:SCR_013179) | sam_comp | software resource | A simple arithmetic coding based compressor for the SAM and BAM (DNA sequence alignment) file format. | c++ |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23533605 | OMICS_00968 | SCR_013179 | 2026-07-25 12:07:45 | 0 | ||||||||
|
HeurAA Resource Report Resource Website |
HeurAA (RRID:SCR_013212) | HeurAA | software resource | Software for accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing. | unix/linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:23349847 | OMICS_00097, biotools:heuraa | https://bio.tools/heuraa | SCR_013212 | heurAA - NGS multiplexed amplicon aligner | 2026-07-25 12:07:46 | 0 | ||||||
|
bisReadMapper Resource Report Resource Website |
bisReadMapper (RRID:SCR_013171) | bisReadMapper | software resource | Fast and lightweight package for mapping bisulfite converted DNA sequencing reads from the Illumina platform. | illumina |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00576 | SCR_013171 | bisReadMapper - Software for dealing with DNA methylation sequencing data | 2026-07-25 12:07:45 | 0 | ||||||||
|
CEDER Resource Report Resource Website 10+ mentions |
CEDER (RRID:SCR_013255) | CEDER | software resource | R package intended to implement a program for detecting differentially expressed genes (DEG) using RNA-Seq by combining significance of exons within a gene. |
is listed by: OMICtools has parent organization: University of Southern California; Los Angeles; USA |
OMICS_01301 | SCR_013255 | 2026-07-25 12:07:46 | 11 | ||||||||||
|
GPSeq Resource Report Resource Website 1+ mentions |
GPSeq (RRID:SCR_013250) | GPSeq | software resource | A software tool to analyze RNA-seq data to estimate gene and exon expression, identify differentially expressed genes, and differentially spliced exons., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools has parent organization: University of Southern California; Los Angeles; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01333 | SCR_013250 | 2026-07-25 12:07:48 | 6 | |||||||||
|
MAP Resource Report Resource Website 1+ mentions |
MAP (RRID:SCR_013216) | software resource | This resource is out of service. Documented on February 23,2021. Software for de novo metagenomic assembly program for shotgun DNA reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Peking University; Beijing; China |
PMID:22495746 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01424, biotools:MAP | https://bio.tools/MAP | SCR_013216 | Metagenomic Assembly Program | 2026-07-25 12:07:46 | 1 | ||||||
|
DiffSplice Resource Report Resource Website 10+ mentions |
DiffSplice (RRID:SCR_013215) | DiffSplice | software resource | The Genome-Wide Detection of Differential Splicing Events with RNA-seq. |
is listed by: OMICtools has parent organization: University of Kentucky; Kentucky; USA |
PMID:23155066 | OMICS_01330 | SCR_013215 | 2026-07-25 12:07:50 | 13 | |||||||||
|
genCAT Resource Report Resource Website 1+ mentions |
genCAT (RRID:SCR_013220) | genCAT | software resource | Software designed as an open platform that allows users to incorporate as many datasets (concepts) as possible to annotate the input gene list, as long as these datasets are prepared in bigwig, BED, BAM/SAM formats. |
is listed by: OMICtools has parent organization: Google Code |
GNU General Public License, v2 | OMICS_01416 | SCR_013220 | gencat - Gene''s Comprehensive Annotation Tool | 2026-07-25 12:07:46 | 6 | ||||||||
|
SOCS Resource Report Resource Website 50+ mentions |
SOCS (RRID:SCR_013223) | SOCS | software resource | Performs ungapped alignment of SOLiD (color space) sequencing reads against reference sequences. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00590 | SCR_013223 | 2026-07-25 12:07:47 | 88 | ||||||||||
|
aCGH Resource Report Resource Website 100+ mentions |
aCGH (RRID:SCR_013232) | aCGH | software resource | Software functions for reading aCGH data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00698 | SCR_013232 | 2026-07-25 12:07:47 | 135 | ||||||||||
|
DSP Resource Report Resource Website |
DSP (RRID:SCR_013114) | DSP | software resource | Pipeline for small genome assembly using SOLiD sequencing technology. |
is listed by: OMICtools has parent organization: SourceForge |
Apache License, v2 | OMICS_00013 | SCR_013114 | denovo_solid_pipeline | 2026-07-25 12:07:48 | 0 | ||||||||
|
RepeatSeq Resource Report Resource Website 10+ mentions |
RepeatSeq (RRID:SCR_013235) | RepeatSeq | software resource | Software that determines genotypes for microsatellite repeats in high-throughput sequencing data. | is listed by: OMICtools | PMID:23090981 | OMICS_00112 | SCR_013235 | 2026-07-25 12:07:46 | 18 | |||||||||
|
Tuxedo Resource Report Resource Website 100+ mentions |
Tuxedo (RRID:SCR_013194) | Tuxedo | software resource | Software that manages the RNA-sequencing pipeline based on the TopHat suite of software automatically. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01415 | SCR_013194 | Tuxedo: Automated RNA-sequencing Pipeline Script | 2026-07-25 12:07:45 | 100 | |||||||||
|
MicroRazerS Resource Report Resource Website 1+ mentions |
MicroRazerS (RRID:SCR_013316) | MicroRazerS | software resource | A software tool optimized for mapping short RNAs onto a reference genome. |
is listed by: OMICtools has parent organization: Free University of Berlin; Berlin; Germany |
PMID:19880369 | OMICS_00371 | SCR_013316 | 2026-07-25 12:07:51 | 5 | |||||||||
|
FusionSeq Resource Report Resource Website 1+ mentions |
FusionSeq (RRID:SCR_013329) | FusionSeq | software resource | A modular framework for finding gene fusions by analyzing Paired-End RNA-Sequencing data. | is listed by: OMICtools | OMICS_01351 | SCR_013329 | 2026-07-25 12:07:48 | 7 | ||||||||||
|
SeqTRACS Resource Report Resource Website |
SeqTRACS (RRID:SCR_013294) | SeqTRACS | software resource | Software for a Laboratory Information Management System (LIMS) for tracking, organizing, and accessing sequencing requests and ABI trace files produced by a centralized sequencing core facility. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v3 | OMICS_01013 | SCR_013294 | SeqTRACS: LIMS for sequencing core facilities | 2026-07-25 12:07:49 | 0 |
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