Tools   Select Another Resource Report Type

http://sourceforge.net/projects/vanator-cvr/

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.

Proper citation: Vanator (RRID:SCR_004370) Copy   

•   Source: SciCrunch Registry

http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/

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.

Proper citation: FastQ Screen (RRID:SCR_000141) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/blastplot/

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.

Proper citation: BLASTPLOT (RRID:SCR_000162) Copy   

•   Source: SciCrunch Registry

http://ribopicker.sourceforge.net/

Software to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets.

Proper citation: riboPicker (RRID:SCR_000360) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/kinannote/

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.

Proper citation: Kinannote (RRID:SCR_000352) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ngs-toolbox/

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.

Proper citation: NGS tools for the novice (RRID:SCR_000664) Copy   

•   Source: SciCrunch Registry

http://www.bsse.ethz.ch/cbg/software/shorah

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.

Proper citation: ShoRAH (RRID:SCR_005211) Copy   

•   Source: SciCrunch Registry

http://maq.sourceforge.net/

A set of programs that map and assemble fixed-length Solexa/SOLiD reads in a fast and accurate way.

Proper citation: Maq (RRID:SCR_005485) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/softsearch/

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).

Proper citation: SoftSearch (RRID:SCR_006683) Copy   

•   Source: SciCrunch Registry

https://github.com/itojal/hot_scan

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.

Proper citation: hot scan (RRID:SCR_002840) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/saskprimerfs/

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.

Proper citation: SaskPrimerFS (RRID:SCR_003159) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/primerdesigner/

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.

Proper citation: JCVI Primer Designer (RRID:SCR_003275) Copy   

•   Source: SciCrunch Registry

https://github.com/akiomiyao/tif

A search program to detect insertions of transposable element from short reads of next generation sequencer.

Proper citation: Transposon Insertion Finder (RRID:SCR_001159) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.mdanderson.org/main/BreakFusion

Software package written in Perl and C++ that provides a computational pipeline for identifying gene fusions from RNA-seq data.

Proper citation: BreakFusion (RRID:SCR_001102) Copy   

•   Source: SciCrunch Registry

http://josephryan.github.io/baa.pl/

Software tool to evaluate de novo genome assemblies with RNA transcripts.

Proper citation: Baa.pl (RRID:SCR_001197) Copy   

•   Source: SciCrunch Registry

http://www.gobics.de/fabian/treephyler.php

A software tool for fast taxonomic profiling of metagenomes.

Proper citation: Treephyler (RRID:SCR_000109) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/cg-pipeline/

A software tool for assembling genome sequence data and running feature prediction and annotation tools on the assembly.

Proper citation: CG-Pipeline (RRID:SCR_000047) Copy   

•   Source: SciCrunch Registry

http://svdetect.sourceforge.net/Site/Home.html

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.

Proper citation: SVDetect (RRID:SCR_010812) Copy   

•   Source: SciCrunch Registry

http://bioinfo.au.tsinghua.edu.cn/software/pcs/

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.

Proper citation: Pairwise Conservation Scores - An Algorithm to Identify Conserved K-mers (RRID:SCR_013409) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/simulatepcr/

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.

Proper citation: Simulate PCR (RRID:SCR_012106) Copy   

•   Source: SciCrunch Registry