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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Vanator Resource Report Resource Website 1+ mentions |
Vanator (RRID:SCR_004370) | Vanator | software resource | A Perl pipeline utilising a large variety of common alignment, assembly and analysis tools to assess the metagenomic profiles of Illumina deep sequencing samples. The emphasis is on the discovery of novel viruses in clinical and environmental samples. | perl, metagenomic, illumina, alignment, assembly, analysis, profile, virus, clinical, environment, next-generation sequencing, taxonomy, read |
is listed by: OMICtools has parent organization: SourceForge has parent organization: University of Glasgow; Glasgow; United Kingdom |
PMID:23296970 | OMICS_01505 | SCR_004370 | Vanator-CVR, Vanator-CVR - A metagenomics & virus discovery pipeline, Virus Alignment de Novo Assembly and Taxonomy On Reads, Vanator-CVR: A metagenomics and virus discovery pipeline | 2025-04-19 06:42:18 | 2 | |||||||
|
FastQ Screen Resource Report Resource Website 10+ mentions |
FastQ Screen (RRID:SCR_000141) | FastQ Screen | software resource | Software that allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect. | perl, FASEB list |
is listed by: OMICtools has parent organization: Babraham Institute |
PMID:30254741 | Free, Freely available | OMICS_01042 | SCR_000141 | 2025-04-19 06:39:31 | 41 | |||||||
|
BLASTPLOT Resource Report Resource Website |
BLASTPLOT (RRID:SCR_000162) | BLASTPLOT | software resource | A PERL module that can quickly plot the BLAST results from short sequences (primers, probes, reads) against reference targets. This software generates PNG graphs for all of the reference sequences associated with a BLAST result set. | perl, blast, short sequence, primer, png, png graph |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24685334 | Open source, Available for download | OMICS_01433 | SCR_000162 | 2025-04-19 06:39:32 | 0 | |||||||
|
riboPicker Resource Report Resource Website 1+ mentions |
riboPicker (RRID:SCR_000360) | software resource | Software to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets. | standalone software, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:22155869 | OMICS_02618, biotools:ribopicker | https://bio.tools/ribopicker | SCR_000360 | 2025-04-19 06:39:43 | 2 | ||||||||
|
Kinannote Resource Report Resource Website 1+ mentions |
Kinannote (RRID:SCR_000352) | software resource | Software that identifies and classifies protein kinases in a user-provided fasta file using an HMM derived from serine / threonine protein kinases, a position specific scoring matrix derived from the HMM, and comparison with a local version of the curated kinase database from kinase.com. | standalone software, perl |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23904509 | BSD License | OMICS_05965 | SCR_000352 | 2025-04-19 06:39:42 | 2 | ||||||||
|
NGS tools for the novice Resource Report Resource Website 1+ mentions |
NGS tools for the novice (RRID:SCR_000664) | NGS tools for the novice | software resource | A collection of simple Perl scripts adressed to scientists doing research that bases on high throughput genomic/transcriptomic data. It does not require any bioinformatic expertise. The scripts perform fundamental processing steps like sorting sequences by TAGs, FASTQ to FASTA conversion, filtering and counting of redundant sequences, individually adjustable FASTQ quality filtering or basic analyses like base count and analysis of sequence length distribution. | next generation sequencing, perl |
is listed by: OMICtools has parent organization: SourceForge |
Academic Free License | OMICS_01063 | SCR_000664 | NGS tools for the novice - Handy tools for processing of next generation sequencing (NGS) data | 2025-04-19 06:40:00 | 3 | |||||||
|
ShoRAH Resource Report Resource Website 10+ mentions |
ShoRAH (RRID:SCR_005211) | ShoRAH | software resource | A software package that allows for inference about the structure of a population from a set of short sequence reads as obtained from ultra-deep sequencing of a mixed sample. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes. | linux, mac os x, windows, next-generation sequencing, c++, python, perl, structure, population, short sequence read, haplotype, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: ETH Zurich; Zurich; Switzerland |
PMID:21521499 | GNU General Public License, v3 | biotools:shorah, OMICS_00231 | https://bio.tools/shorah | SCR_005211 | Short Reads Assembly into Haplotypes, ShoRAH - Short Reads Assembly into Haplotypes | 2025-04-19 06:42:46 | 33 | |||||
|
Maq Resource Report Resource Website 50+ mentions |
Maq (RRID:SCR_005485) | Maq | software resource | A set of programs that map and assemble fixed-length Solexa/SOLiD reads in a fast and accurate way. | command-line, curses/ncurses, opengl, c, c++, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: SourceForge |
DOI:10.1101/gr.078212.108 | GNU General Public License, v2 | biotools:maq, OMICS_00668 | https://bio.tools/maq https://sources.debian.org/src/maq/ |
SCR_005485 | mapass2, Mapping and Assembly with Quality, Mapping and Assembly with Qualities, Maq: Mapping and Assembly with Qualities | 2025-04-19 06:42:53 | 66 | |||||
|
SoftSearch Resource Report Resource Website 1+ mentions |
SoftSearch (RRID:SCR_006683) | SoftSearch | software resource | A sensitive structural variant (SV) detection software tool for Illumina paired-end next-generation sequencing data. It simultaneously utilizes soft-clipping and read-pair strategies for detecting SVs to increase sensitivity. Soft clips are proxies for split-reads that indicate part of the read maps to the reference genome, but the other part is not localized at the same place (e.g. breakpoint spanning reads). Discordant read-pairs refer to a read and its mate, where the insert size is greater (or less than) the expected distribution of the dataset ? or ? where the mapping orientation of the reads is unexpected (e.g. both on the same strand). SoftSearch looks for areas with soft-clipping in the genome that have discordant read pairs supporting the anomaly. Once areas with both these conditions are identified, the read and mate information is extracted directly from the BAM file containing the discordant reads, obviating the need for time-consuming and error-prone complex alignment strategies. Only a small number of soft-masked bases discordant read-pairs are necessary to identify an SV, which on their own would not be sufficient to make an SV call, thus highlighting SoftSearch?s improved sensitivity. SoftSearch is well suited to be ?plugged in? to most sequence analysis workflows, since it requires standard file inputs, such as a BAM file using almost any aligner and a reference genome FASTA file. Because SoftSearch requires soft-masked bases, the only requirement is that the aligner must have this functionality, which is usually turned on by default by many standard aligners (e.g. BWA, Novoalign, etc). | illumina, structural variant, next-generation sequencing, perl, academic |
is listed by: OMICtools has parent organization: Google Code |
GNU General Public License, v2 | OMICS_00322 | SCR_006683 | SoftSearch - Detecting Structural Variations Using Split Reads and Discordant Read Pairs | 2025-04-19 06:43:41 | 5 | |||||||
|
hot scan Resource Report Resource Website 1+ mentions |
hot scan (RRID:SCR_002840) | software resource | A free software to detect genomic regions unusually rich in translocation breakpoints. More generally, it may be used to detect a region that is unusually rich in a given character of a binary sequence. | software package, perl, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24860160 | GNU General Public License, v2 | biotools:hot_scan, OMICS_05200 | https://bio.tools/hot_scan | SCR_002840 | hot_scan | 2025-04-19 06:41:25 | 2 | ||||||
|
SaskPrimerFS Resource Report Resource Website |
SaskPrimerFS (RRID:SCR_003159) | SaskPrimerFS | software resource | Software pipeline for designing gene family specific PCR primers. It infers intronic regions of a target species and design for them by utilizing DNA sequence information from a reference organism. | gene family, pcr primer, pcr, primer, dna sequence, command-line, perl |
is listed by: OMICtools has parent organization: SourceForge |
GNU Lesser General Public License, v3 | OMICS_02335 | SCR_003159 | 2025-04-19 06:41:36 | 0 | ||||||||
|
JCVI Primer Designer Resource Report Resource Website 1+ mentions |
JCVI Primer Designer (RRID:SCR_003275) | JCVI Primer Designer | software resource | High throughput PCR primer design software. Target regions defined through a rich set of descriptors, such as Ensembl accessions and arbitrary genomic coordinates, may be specified. Primer pairs are then selected computationally to produce a minimal amplicon set capable of tiling across the specified target regions. As part of the tiling process, primer pairs are computationally screened to meet the criteria for success with one of two PCR amplification protocols. | perl, command-line, pcr primer design, pcr, primer, high throughput sequencing |
is listed by: OMICtools has parent organization: SourceForge |
PMID:18405373 | GNU General Public License, v2 | OMICS_02330 | SCR_003275 | 2025-04-19 06:41:38 | 1 | |||||||
|
Transposon Insertion Finder Resource Report Resource Website 1+ mentions |
Transposon Insertion Finder (RRID:SCR_001159) | TIF | software resource | A search program to detect insertions of transposable element from short reads of next generation sequencer. | perl, unix/linux | is listed by: OMICtools | PMID:24629057 | OMICS_03508 | SCR_001159 | Transposon Insertion Finder | 2025-04-19 06:40:22 | 1 | |||||||
|
BreakFusion Resource Report Resource Website 1+ mentions |
BreakFusion (RRID:SCR_001102) | BreakFusion | software resource | Software package written in Perl and C++ that provides a computational pipeline for identifying gene fusions from RNA-seq data. | computational pipeline, gene fusions, rna, sequence, data, perl, c++ |
is listed by: OMICtools has parent organization: University of Texas MD Anderson Cancer Center |
PMID:22563071 DOI:10.1093/bioinformatics/bts272 |
Open source, Available for download | OMICS_01342 | SCR_001102 | 2025-04-19 06:40:21 | 3 | |||||||
|
Baa.pl Resource Report Resource Website |
Baa.pl (RRID:SCR_001197) | Baa.pl | software resource | Software tool to evaluate de novo genome assemblies with RNA transcripts. | genomics, genome assembly, rna transcript, perl | is listed by: OMICtools | GNU General Public License, v3, Acknowledgement requested | OMICS_02154 | https://github.com/josephryan/baa.pl | SCR_001197 | 2025-04-19 06:40:23 | 0 | |||||||
|
Treephyler Resource Report Resource Website 1+ mentions |
Treephyler (RRID:SCR_000109) | Treephyler | software resource | A software tool for fast taxonomic profiling of metagenomes. | metagenome, perl, nucleotide, protein, next-generation sequencing | is listed by: OMICtools | PMID:20172941 | Acknowledgement requested, Free, Public | OMICS_01469 | SCR_000109 | Treephyler: fast taxonomic profiling of metagenomes | 2025-04-19 06:39:29 | 1 | ||||||
|
CG-Pipeline Resource Report Resource Website |
CG-Pipeline (RRID:SCR_000047) | software resource | A software tool for assembling genome sequence data and running feature prediction and annotation tools on the assembly. | perl | has parent organization: SourceForge | PMID:20519285 | GNU General Public License | OMICS_04062 | SCR_000047 | 2025-04-19 06:39:26 | 0 | ||||||||
|
SVDetect Resource Report Resource Website 10+ mentions |
SVDetect (RRID:SCR_010812) | SVDetect | software resource | Software application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies. This tool aims to identify structural variations with both clustering and sliding-window strategies, and helping in their visualization at the genome scale. It is compatible with SOLiD and Illumina (>=1.3) reads. | structural variation, sequencing, chromosomal rearrangement, high-throughput sequencing, solid, illumina, genome, insertion, deletion, inversion, duplication, translocation, command-line, perl, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Curie Institute; Paris; France |
PMID:20639544 | GNU General Public License, v3 | OMICS_00324, biotools:svdetect | https://bio.tools/svdetect | SCR_010812 | SVDetect: a tool to detect genomic structural variations from paired-end and mate-pair sequencing data | 2025-04-19 06:45:10 | 22 | |||||
|
Pairwise Conservation Scores - An Algorithm to Identify Conserved K-mers Resource Report Resource Website 1+ mentions |
Pairwise Conservation Scores - An Algorithm to Identify Conserved K-mers (RRID:SCR_013409) | PCS | software resource | A stand-alone package to identify and analyze conserved k-mers in pairwise alignment. This program shows high performance for identifying miRNA seed binding sites in 3''-UTRs. | perl, perl script, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Tsinghua University; Beijing; China |
biotools:pcs, nlx_33020 | https://bio.tools/pcs | http://bioinfo.au.tsinghua.edu.cn/member/~gujin/pcs/ | SCR_013409 | Pairwise Conservation Scores | 2025-04-19 06:46:43 | 3 | ||||||
|
Simulate PCR Resource Report Resource Website |
Simulate PCR (RRID:SCR_012106) | software resource | Software that can be run from the command line for high throughput applications which can calculate all products from large lists of primers and probes compared to a large sequence database such as nt. | standalone software, perl |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25005023 | Free, Public | OMICS_05372 | SCR_012106 | 2025-04-19 06:46:06 | 0 |
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