Nesoni 0.132 – Swiss Army Knife for NGS SNP calling / RNA-Seq DGE / Read Cleaning

Nesoni 0.132

:: DESCRIPTION

Nesoni is a high-throughput sequencing data analysis toolset, which the VBC has developed to cope with the flood of Illumina, 454, and SOLiD data now being produced.

::DEVELOPER

Victorian Bioinformatics Consortium

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 Nesoni

:: MORE INFORMATION

ACCUSA 20140930 / ACCUSA2 – (Multi-purpose) SNP Calling on Draft Genomes

ACCUSA 20140930 / ACCUSA2

:: DESCRIPTION

ACCUSA is designed for accurate SNP calling on draft genome sequences.The main objective is to rule out pseudo SNPs where the reference genome has low sequencing base quality. This is obtained using a Bayesian framework considering the base quality values of the resequencing reads as well as the base quality of the reference genome.

ACCUSA2: Multi-purpose SNV calling enhanced by probabilistic integration of quality scores

::DEVELOPER

BIMSB Bioinformatics Core.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java 

:: DOWNLOAD

  ACCUSA , ACCUSA2

:: MORE INFORMATION

Citation:

Bioinformatics. 2010 May 15;26(10):1364-5. Epub 2010 Apr 1.
ACCUSA–accurate SNP calling on draft genomes.
Fröhler S, Dieterich C.

Bioinformatics. 2013 Jul 15;29(14):1809-10. doi: 10.1093/bioinformatics/btt268. Epub 2013 May 16.
ACCUSA2: multi-purpose SNV calling enhanced by probabilistic integration of quality scores.
Piechotta M, Dieterich C.

Biscap and cfdr 0.11 – Scripts for post-alignment Snp-calling and Verification

Biscap and cfdr 0.11

:: DESCRIPTION

Biscap and cfdr is a script for determining homozygous and heterozygous positions from an alignment using binomial probabilities from a predicted error rate (BiSCaP) and a method to benchmark the accuracy of this and other alignment/SNP-calling methods (cFDR)

::DEVELOPER

Biscap and cfdr team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Perl

:: DOWNLOAD

 Biscap and cfdr

:: MORE INFORMATION

Citation

Sci Rep. 2013;3:1512. doi: 10.1038/srep01512.
Using false discovery rates to benchmark SNP-callers in next-generation sequencing projects.
Farrer RA1, Henk DA, MacLean D, Studholme DJ, Fisher MC.

Virmid 1.1.1 – Virtual Microdissection for SNP Calling

Virmid 1.1.1

:: DESCRIPTION

Virmid  is a Java based variant caller designed for disease-control matched samples. Virmid is also specialized for identifying potential within individual contamination where the disease sample cannot be purified enough. While the SNP calling rate is severely compromised with this heterogeneity, Virmid can uncover SNPs with low allele frequency by considering the level of contamination (alpha)

::DEVELOPER

Virmid team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Java

:: DOWNLOAD

 Virmid

:: MORE INFORMATION

Citation

Genome Biol. 2013 Aug 29;14(8):R90. [Epub ahead of print]
Virmid: accurate detection of somatic mutations with sample impurity inference.
Kim S, Jeong K, Bhutani K, Lee JH, Patel A, Scott E, Nam H, Lee H, Gleeson JG, Bafna V.

M3 20121207 – SNP Calling Algorithm for Illumina BeadArry Data

M3 20121207

:: DESCRIPTION

M3 (modified mixture model) is an improved SNP calling algorithm for Illumina BeadArray Data

::DEVELOPER

Zhao Hongyu’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Matlab

:: DOWNLOAD

 M3

:: MORE INFORMATION

Citation

Li, G.X. J. Gelernter, H.R. Kranzler and H.Y. Zhao (2011).
M3: An Improved SNP Calling Algorithm for Illumina BeadArray Data.
Bioinformatics (2011)doi: 10.1093/bioinformatics/btr6

UMAKE 1.0.1 – SNP Calling Pipeline

UMAKE 1.0.1

:: DESCRIPTION

UMAKE is a software pipeline to detect SNPs and call their genotypes from a list of BAM files. UMAKE pipeline has been successfully applied in detecting SNPs from many large-scale next-generation sequencing studies.

:DEVELOPER

Hyun Min Kang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler
:: DOWNLOAD

 UMAKE

:: MORE INFORMATION

SliderII 1.1 – High Quality SNP Calling Using Illumina Data at Shallow Coverage

SliderII 1.1

:: DESCRIPTION

SliderII Results of SNPs concordance comparison to Maq.We used 68 lanes human whole genome shotgun sequencing, WGSS, PET data (real data), a total of 906 million reads sizes from 36 to 42 bases, using each of SliderII and MAQ, we aligned these reads to the human genome hg18 resulting a coverage of about 7.5 X. For each aligner, SNPs are sorted in descending order, using SNPs score for SliderII, and the Phred-like consensus quality score for MAQ.  Concordance with Ensembl Variation 50 SNPs is used to compare SNPs calling accuracy.

::DEVELOPER

Yaron Butterfield

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX

:: DOWNLOAD

 SliderII

:: MORE INFORMATION

Citation

Malhis et. al. 2008
High Quality Alignment and SNP Calling for Illumina High Throughput Sequence Data
Bioinformatics (2009) 25 (1): 6-13