discoSnp 2.5.4 – Discovering SNPs without requiring any reference Genome

discoSnp 2.5.4

:: DESCRIPTION

Software discoSnp is designed for discovering Single Nucleotide Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation Sequencers (NGS).

::DEVELOPER

Genome Analysis Toolbox with de-Bruijn graph (GATB)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

discoSnp

:: MORE INFORMATION

Citation

Mol Ecol Resour. 2014 Mar;14(2):393-400. doi: 10.1111/1755-0998.12179. Epub 2013 Nov 11.
Development of genomic resources for the tick Ixodes ricinus: isolation and characterization of single nucleotide polymorphisms.
Quillery E1, Quenez O, Peterlongo P, Plantard O.

AllelePipe 1.0.28 – Identifying Alleles in Population Genomic datasets without a Reference Genome

AllelePipe 1.0.28

:: DESCRIPTION

AllelePipe is a pipeline to cluster putative alleles within and among individuals. AllelePipe is designed specifically for cases in which read depth information is not appropriate or available to assist with disentangling closely related paralogs from allelic variation, as in transcriptome or previously assembled libraries.

::DEVELOPER

The Dlugosch Lab @ The University of Arizona

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

AllelePipe

:: MORE INFORMATION

Citation

G3 (Bethesda). 2013 Feb;3(2):359-67. doi: 10.1534/g3.112.003871.
Allele identification for transcriptome-based population genomics in the invasive plant Centaurea solstitialis.
Dlugosch KM, Lai Z, Bonin A, Hierro J, Rieseberg LH.

SlideSort-BPR 1.0.0 – Finding Differences between Multiple Short-read datasets without Reference Genome

SlideSort-BPR 1.0.0

:: DESCRIPTION

SlideSort-BPR is based on a fast algorithm for all-against-all comparisons of short reads and theoretical analyses of the number of neighboring reads

:: DEVELOPER

SlideSort-BPR Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

SlideSort-BPR

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 29. pii: btu360. [Epub ahead of print]
Reference-free Prediction of Rearrangement Breakpoint Reads.
Wijaya E1, Shimizu K2, Asai K3, Hamada M

UnoSeq 1.0 – Expression Profiling with Next Generation Sequencing without a Reference Genome

UnoSeq 1.0

:: DESCRIPTION

UnoSeq is a Java library to analyze next generation sequencing data (e.g. data generated by Illumina’s mRNAseq method) and especially perform expression profiling in organisms where no well-annotated reference genome exists.

::DEVELOPER

UnoSeq team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / Mac OsX.
Java
Bowtie
Velvet
BLAST

:: DOWNLOAD

UnoSeq

:: MORE INFORMATION

Citation

Into the unknown: expression profiling without genome sequence information in CHO by next generation sequencing.
Birzele F, Schaub J, Rust W, Clemens C, Baum P, Kaufmann H, Weith A, Schulz TW, Hildebrandt T.
Nucleic Acids Res. 2010 Jul;38(12):3999-4010. doi: 10.1093/nar/gkq116.

NextGenMap 0.5.5 – Map NGS Reads against a Reference Genome

NextGenMap 0.5.5

:: DESCRIPTION

NextGenMap/NGM (Next Generation Mapper)is a computer program to map NGS reads against a reference genome using CPUs or GPUs.

::DEVELOPER

the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

NextGenMap

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Nov 1;29(21):2790-1. doi: 10.1093/bioinformatics/btt468.
NextGenMap: fast and accurate read mapping in highly polymorphic genomes.
Sedlazeck FJ, Rescheneder P, von Haeseler A.

DNAzip – DNA Sequence Compression using a Reference Genome

DNAzip

:: DESCRIPTION

DNAzip is a series of techniques that in combination reduces a single genome to a size small enough to be sent as an email attachment.

::DEVELOPER

Xiaohui Xie and Chen Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C Compiler

:: DOWNLOAD

DNAzip

:: MORE INFORMATION

Citation:

Bioinformatics. 2009 Jan 15;25(2):274-5. Epub 2008 Nov 7.
Human genomes as email attachments.
Christley S, Lu Y, Li C, Xie X.