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http://ftp://ftp.ieeta.pt/~ap/codecs/GReEn1.tar.gz
A compression tool recently proposed for compressing genome resequencing data using a reference genome sequence., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: GReEn (RRID:SCR_009264) Copy
https://github.com/lpantano/seqbuster
Software tool for processing and analysis of small RNAs datasets.Reveals ubiquitous miRNA modifications in human embryonic cells.
Proper citation: SeqBuster (RRID:SCR_009616) Copy
http://omicslab.genetics.ac.cn/ISRNA/
An online toolkit for analyzing high-throughput small RNA sequencing data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: ISRNA (RRID:SCR_009565) Copy
http://users-mb.au.dk/pmgrp/downloads.php
A pipeline for small RNA-seq data analysis.
Proper citation: shortran (RRID:SCR_009636) Copy
http://scalce.sourceforge.net/Home
A FASTQ compression tool that uses locally consistent parsing to obtain better compression rate.
Proper citation: SCALCE (RRID:SCR_009658) Copy
http://genome.sph.umich.edu/wiki/Generic_Exome_Analysis_Plan
Outline of a generic plan for analysis of a whole exome sequencing project.
Proper citation: Generic Exome Analysis Plan (RRID:SCR_009656) Copy
http://www.labmedmolge.unisa.it/inglese/research/imir
A modular pipeline for comprehensive analysis of smallRNA-Seq data, comprising specific tools for adapter trimming, quality filtering, DE analysis, target prediction by integrating multiple open source modules and resources in an automated workflow.
Proper citation: iMir (RRID:SCR_009496) Copy
http://www.stanford.edu/group/wonglab/SpliceMap/
A de novo splice junction discovery and alignment tool.
Proper citation: SpliceMap (RRID:SCR_009650) Copy
http://www.allseq.com/default.aspx
Free online tools to find the best Sequencing Service provider for your project.
Proper citation: AllSeq (RRID:SCR_010053) Copy
http://dna.engr.uconn.edu/?page_id=105
Software package that can be used to infer isoform and gene expression levels from high-throughput transcriptome sequencing (RNA-Seq) data.
Proper citation: IsoEM (RRID:SCR_009993) Copy
http://code.google.com/p/bitseq/
A software application for inferring expression levels of individual transcripts from sequencing (RNA-Seq) data and estimating differential expression (DE) between conditions.
Proper citation: BitSeq (RRID:SCR_009904) Copy
http://bioen-compbio.bioen.illinois.edu/TrueSight/
Self-training Algorithm for Splice Junction Detection using RNA-seq.
Proper citation: TrueSight (RRID:SCR_009835) Copy
A cross-platform software program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.
Proper citation: BEAST (RRID:SCR_010228) Copy
http://hkbic.cuhk.edu.hk/software/abmapper
A portable, easy-to-use package for spliced alignment, junction site detection, and reads mapping. The core module was written in C++ and wrapped in PERL scripts.
Proper citation: ABMapper (RRID:SCR_010242) Copy
http://htsvipr.sourceforge.net/
A software program to screen for sequence variants (SNPs, deletions) in sequence data generated by high-throughput-sequencing platforms.
Proper citation: vipR (RRID:SCR_010685) Copy
http://www.genome.umd.edu/masurca.html
A whole genome assembly software that combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: MaSuRCA (RRID:SCR_010691) Copy
http://bioinformatics.research.nicta.com.au/software/gossamer/
A software application for the de novo assembly of genomes from fragments of DNA that specifically attacks the question of scalability.
Proper citation: Gossamer (RRID:SCR_010612) Copy
http://www.bcgsc.ca/platform/bioinfo/software/abyss
Software providing de novo, parallel, paired-end sequence assembler that is designed for short reads. ABySS 1.0 originally showed that assembling human genome using short 50 bp sequencing reads was possible by aggregating half terabyte of compute memory needed over several computers using standardized message passing system. ABySS 2.0 is Resource Efficient Assembly of Large Genomes using Bloom Filter. ABySS 2.0 departs from MPI and instead implements algorithms that employ Bloom filter, probabilistic data structure, to represent de Bruijn graph and reduce memory requirements.
Proper citation: ABySS (RRID:SCR_010709) Copy
http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0023501
An algorithm for de novo genome assembly with short paired-end reads.
Proper citation: Meraculous (RRID:SCR_010700) Copy
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
Allow the high-performance display of next-generation sequencing experiment results in the UCSC Genome Browser.
Proper citation: BigWig and BigBed (RRID:SCR_007708) Copy
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