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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
http://sourceforge.net/projects/xorro-overlap/
Efficient paired-read overlap software program for use with Illumina sequencing.
Proper citation: XORRO (RRID:SCR_003181) Copy
http://compbio.cs.sfu.ca/software-novelseq
Software pipeline to detect novel sequence insertions using high throughput paired-end whole genome sequencing data.
Proper citation: NovelSeq (RRID:SCR_003136) Copy
http://sourceforge.net/projects/gbsbarcode/
PERL script used to split barcode of Illumina sequencing data created by GBS protocol (www.maizegenetics.net). The barcode has variable size. Paired-end reads are supported.
Proper citation: GBS barcode splitter (RRID:SCR_006799) Copy
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
http://sourceforge.net/projects/ngopt/
Software that produces high quality microbial genome assemblies on a laptop computer without any parameter tuning. A5-miseq does this by automating the process of adapter trimming, quality filtering, error correction, contig and scaffold generation, and detection of misassemblies. Unlike the original A5 pipeline, A5-miseq can use long reads from the Illumina MiSeq, use read pairing information during contig generation, and includes several improvements to read trimming.
Proper citation: A5-miseq (RRID:SCR_012148) Copy
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
http://sourceforge.net/projects/skewer/
Software program for adapter trimming that is specially designed for processing Illumina paired-end sequences.
Proper citation: skewer (RRID:SCR_001151) Copy
http://uc-echo.sourceforge.net/
Error correction algorithm designed for short-reads from next-generation sequencing platforms such as Illumina''s Genome Analyzer II.
Proper citation: ECHO (RRID:SCR_011851) Copy
http://sourceforge.net/projects/cgap-align/
A time efficient read alignment tool built on the top of BWA.
Proper citation: CGAP-Align (RRID:SCR_000350) Copy
http://sourceforge.net/projects/particlecall/
A base-calling algorithm for Illumina DNA sequencing.
Proper citation: ParticleCall (RRID:SCR_001103) Copy
http://sourceforge.net/projects/abmining/
Python scripts to analyze antibody libraries sequenced by next generation sequencing methods (454, Ion Torrent, MiSeq).
Proper citation: AbMining ToolBox (RRID:SCR_000090) Copy
http://sourceforge.net/projects/trowel-ec/
An error correction module for Illumina sequencing reads, which is based on the k-mer spectrum approach.
Proper citation: Trowel (RRID:SCR_012890) Copy
http://sourceforge.net/projects/bisreadmapper/
Fast and lightweight package for mapping bisulfite converted DNA sequencing reads from the Illumina platform.
Proper citation: bisReadMapper (RRID:SCR_013171) Copy
http://sourceforge.net/projects/virtools/
Software for a low frequency Virus Variant detection pipeline for Illumina data.
Proper citation: VirVarSeq (RRID:SCR_012116) Copy
http://sourceforge.net/projects/imsat/
A python program that uses the polymorphism data obtained from mapping individual Illumina sequence reads onto a reference genome to identify polymorphic STRs.
Proper citation: iMSAT (RRID:SCR_012135) Copy
http://sourceforge.net/projects/htqc/
A software toolkit including statistics tool for illumina high-throughput sequencing data, and filtration tools for sequence quality, length, tail quality, etc..
Proper citation: HTQC (RRID:SCR_006448) Copy
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