Tools   Select Another Resource Report Type

http://bioinf.spbau.ru/quast

Quality assessment software tool for evaluating and comparing genome assemblies. It works both with and without a given reference genome. It produces many reports, summary tables and plots.

Proper citation: QUAST (RRID:SCR_001228) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/kanalyze/

A Java toolkit designed to convert DNA and RNA sequences into k-mers.

Proper citation: KAnalyze (RRID:SCR_001323) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/baccontigeditor/

A simple sequence alignment editing tool, written in Java.

Proper citation: BACContigEditor (RRID:SCR_001617) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/dnaclust/

Software program for clustering large number of short similar DNA sequences. It was originally designed for clustering targeted 16S rRNA pyrosequencing reads.

Proper citation: DNACLUST (RRID:SCR_001771) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/polgui/

An interface between MATLAB and the Polhemus Fastrak digitizer used to digitize fiducial locations and scalp EEG electrode locations. There are 5 versions all of which work under MATLAB R14 (on both linux and windows platforms), # polgui_ver1_r14 : works with 1 receiver (stylus pen) # polgui_ver2_r14 : works with 2 receivers (including the pen) # polgui_ver3_r14 : works with 3 receivers(including the pen) # polgui_ver4_r14 : works with 4 receivers (including the pen) # polgui_ver5_r14 : Generic version which works with 1/2/3/4 receivers (WARNING: Ver 5 might be buggy; not fully tested) Requirements: MATLAB R14 (Linux/Windows)

Proper citation: POLGUI - Matlab Polhemus Interface (RRID:SCR_006752) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/mubiomics/

A set of scripts (mostly python) for processing reads generated by the Roche 454 or Illumina next-gen sequencing platforms. Included are quality control, read demultiplexing and microbiome characterisation scripts for use with usearch, pplacer and RDP classifier.

Proper citation: mubiomics (RRID:SCR_006785) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/qudaich/

A software package for local sequence alignment for next-generation sequencing (NGS) data. It generates the pairwise local alignments between a query dataset against a database. The main design purpose of qudaich is to focus on datasets from next generation sequencing. These the datasets generally have hundreds of thousand sequences or more, and so, the input database should contain large number of sequences. Qudaich is flexible and its algorithmic structure imposes no restriction on the absolute limit of the acceptable read length, but the current version of qudaich allow read length <2000 bp. Qudaich can be used to align DNA, translated DNA and protein sequences.

Proper citation: Qudaich (RRID:SCR_006775) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/bamstats/

A GUI desktop tool for calculating and displaying metrics to assess the success of Next Generation Sequencing mapping tools. BAMstats is written in Java and based around the Picard API.

Proper citation: BAMStats (RRID:SCR_006973) Copy   

•   Source: SciCrunch Registry

http://seqbarracuda.sourceforge.net/

A sequence mapping software that utilizes the massive parallelism of graphics processing units to accelerate the inexact alignment of short sequence reads to a particular location on a reference genome. It can align a paired-end library containing 14 million pairs of 76bp reads to the Human genome in about 27 minutes (from fastq files to SAM alignment) using a ��380 NVIDIA Geforce GTX 680*. The alignment throughput can be boosted further by using multiple GPUs (up to 8) at the same time. Being based on BWA (http://bio-bwa.sf.net) from the Sanger Institute, BarraCUDA delivers a high level of alignment fidelity and is comparable to other mainstream alignment programs. It can perform gapped alignment with gap extensions, in order to minimise the number of false variant calls in re-sequencing studies.

Proper citation: BarraCUDA (RRID:SCR_006881) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/taipan/

A fast hybrid short-read assembly tool.

Proper citation: Taipan (RRID:SCR_007330) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ms-spectre/

Software that provides (Quantitiave) analysis of multiple ls-ms(ms) runs, using mzXML import of raw data coming from spectrometers.

Proper citation: MS-Spectre (RRID:SCR_000266) 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://sourceforge.net/projects/gemsim/

A software package for generating realistic simulated next-generation genome sequencing reads with quality score values. The software is written in Python with a command-line user interface.

Proper citation: GemSIM (RRID:SCR_000167) 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://parsecnv.sourceforge.net/

Software that takes CNV calls as input and creates SNP based statistics for CNV occurrence in cases and controls then calls CNVRs based on neighboring SNPs of similar significance.

Proper citation: ParseCNV (RRID:SCR_000355) 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/jnomics/

A collection of cloud-scale DNA sequence analysis tools.

Proper citation: Jnomics (RRID:SCR_000348) Copy   

•   Source: SciCrunch Registry

http://proteinprophet.sourceforge.net/

Software that automatically validates protein identifications made on the basis of peptides assigned to MS/MS spectra by database search programs such as SEQUEST.

Proper citation: ProteinProphet (RRID:SCR_000286) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/fqzcomp/

A basic fastq compressor, designed primarily for high performance.

Proper citation: fqzcomp (RRID:SCR_000299) Copy   

•   Source: SciCrunch Registry