Tag: Mapping

SIRAH 2.2 – Mapping, Backmapping and Visualization of Coarse-grained Models

SIRAH 2.2

:: DESCRIPTION

SIRAH Tools (Southamerican Initiative for a Rapid and Accurate Hamiltonian) comprises a set of utilities to convert all-atoms coordinates to arbitrary residue-based CG schemes, write GROMACS’ topological information at any resolution into PSF format and a VMD plugin to visualize, analyze and retrieve pseudo-atomistic information from CG trajectories performed with the SIRAH force field.

::DEVELOPER

SIRAH team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX
  • AMBER/ GROMACS

:: DOWNLOAD

 SIRAH

:: MORE INFORMATION

Citation

Bioinformatics. 2016 Jan 14. pii: btw020.
SIRAH Tools: mapping, backmapping and visualization of coarse-grained models.
Machado M, Pantano S

PrediXcan – Gene-based Association method for Mapping Traits

PrediXcan

:: DESCRIPTION

PrediXcan is a gene-based association test that prioritizes genes that are likely to be causal for the phenotype.

::DEVELOPER

Gamazon Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • R / Python

:: DOWNLOAD

PrediXcan

 :: MORE INFORMATION

Citation

Gamazon ER, Wheeler HE, Shah KP, Mozaffari SV, Aquino-Michaels K, Carroll RJ, Eyler AE, Denny JC; GTEx Consortium, Nicolae DL, Cox NJ, Im HK.
A gene-based association method for mapping traits using reference transcriptome data.
Nat Genet. 2015 Sep;47(9):1091-8. doi: 10.1038/ng.3367. Epub 2015 Aug 10. PMID: 26258848; PMCID: PMC4552594.

SeqTrimMap 1.0 – Sequential Trimming and Mapping of Short Reads

SeqTrimMap 1.0

:: DESCRIPTION

SeqTrimMap is a script for efficient mapping of short reads from high-thoughput sequencing experiments.

::DEVELOPER

SGJlab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SeqTrimMap

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Feb 1;28(3):318-23. doi: 10.1093/bioinformatics/btr686
Detection of microRNAs in color space.
Marco A, Griffiths-Jones S.

Maq 0.7.1 – Mapping and Assembly with Qualities

Maq 0.7.1

:: DESCRIPTION

Maq stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences.

::DEVELOPER

Heng Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Maq

:: MORE INFORMATION

Citation:

Mapping short DNA sequencing reads and calling variants using mapping quality scores.
Li H, Ruan J, Durbin R.
Genome Res. 2008 Nov;18(11):1851-8.

normGAM – Remove Systematic Biases in Genome Architecture Mapping data

normGAM

:: DESCRIPTION

normGAM is an R package for normalizing genome architecture mapping (GAM) data. It implements five normalization methods, including normalized linkage disequilibrium (NLD), vanilla coverage (VC), sequential component normalization (SCN), iterative correction and eigenvector decomposition (ICE), and Knight-Ruiz 2-norm (KR2). The normalization procedure can remove known and unknown systematic biases, the known biases including window detection frequency, fragment length, mappability, and GC content.

::DEVELOPER

Z. WANG LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

normGAM

:: MORE INFORMATION

Citation

Liu T, Wang Z.
normGAM: an R package to remove systematic biases in genome architecture mapping data.
BMC Genomics. 2019 Dec 30;20(Suppl 12):1006. doi: 10.1186/s12864-019-6331-8. PMID: 31888469; PMCID: PMC6936146.

BisPin and BFAST-Gap – Mapping Bisulfite-Treated Reads

BisPin and BFAST-Gap

:: DESCRIPTION

BFAST-Gap is a modification of the BFAST short DNA read trimmer. BFAST-Gap adds functionality for Ion Torrent DNA reads.

BisPin is a Python 2.7 program that uses BFAST-Gap (or BFAST) to map bisulfite-treated short DNA reads to a reference genome. It supports the hairpin construction strategy and rescores ambiguously mapped reads. Its default alignment scoring function is biologically motivated.

::DEVELOPER

Professor Zhang Liqing’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

BisPin

:: MORE INFORMATION

Citation

BisPin and BFAST-Gap: Mapping Bisulfite-Treated Reads
Jacob Porter, Liqing Zhang
bioRxiv 284596; doi: https://doi.org/10.1101/284596

Hobbes 3.0 – Genome Sequence Mapping

Hobbes 3.0

:: DESCRIPTION

Hobbes is a software package for efficiently mapping DNA snippets (reads) against a reference DNA sequence. It can map short and long reads, and supports Hamming distance (only substitutions) and edit distance (substitutions/insertions/deletions). Hobbes accepts both single-end and paired-end reads for alignment, and can run on multiple CPU cores using multithreading.

::DEVELOPER

CBCL Lab (Computational Biology and Computational Learning) @ UCI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 Hobbes

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2014 Feb 5;15:42. doi: 10.1186/1471-2105-15-42.
Improving read mapping using additional prefix grams.
Kim J, Li C, Xie X

Nucleic Acids Res. 2012 Mar;40(6):e41. doi: 10.1093/nar/gkr1246. Epub 2011 Dec 22.
Hobbes: optimized gram-based methods for efficient read alignment.
Ahmadi A, Behm A, Honnalli N, Li C, Weng L, Xie X.

RazerS 3.5.8 – Fast Read Mapping with Sensitivity Control

RazerS 3.5.8

:: DESCRIPTION

RazerS is a tool for mapping millions of short genomic reads onto a reference genome. It was designed with focus on mapping next-generation sequencing reads onto whole DNA genomes. RazerS searches for matches of reads with a percent identity above a given threshold, whereby it detects matches with mismatches as well as gaps.

RazerS uses a k-mer index of all reads and counts common k-mers of reads and the reference genome in parallelograms. Each parallelogram with a k-mer count above a certain threshold triggers a verification. On success, the genomic subsequence and the read number are stored and written to the output file.

::DEVELOPER

David Weese

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac / Windows

:: DOWNLOAD

RazerS

:: MORE INFORMATION

Citation

RazerS – Fast Read Mapping with Sensitivity Control
David Weese, Anne-Katrin Emde, Tobias Rausch, Andreas Döring, and Knut Reinert
Genome Research, Sep 2009, 19: pp. 1646-1654

Bioinformatics. 2012 Oct 15;28(20):2592-9. doi: 10.1093/bioinformatics/bts505.
RazerS 3: faster, fully sensitive read mapping.
Weese D, Holtgrewe M, Reinert K.

SAMPLE 20090428 – Shadow Autozygosity MaPping by Linkage Exclusion

SAMPLE 20090428

:: DESCRIPTION

SAMPLE is designed to identify regions that are linked to a recessive disease by analysing genotype data from the parents and unaffected sibs of affected individuals. Since this analysis does not use data from affected patients, it is suited to the identification of lethal recessive genes, when the patients may have died before DNA samples could be obtained.

::DEVELOPER

Ian’s DNA@Leeds

:: SCREENSHOTS

SAMPLE

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0 

:: DOWNLOAD

 SAMPLE

:: MORE INFORMATION

Citation

Carr IM, Szymanska K, Sheridan E, Markham AF, Bonthron DT, Johnson CA (2009).
Shadow autozygosity mapping by linkage exclusion (SAMPLE): a simple strategy to identify the genetic basis of lethal autosomal recessive disorders.
Hum Mutat 30: 1642-1649.

AutoSNPa 20121128 – Visual analysis of SNP data for autozygosity Mapping

AutoSNPa 20121128

:: DESCRIPTION

AutoSNPa aids the identification of regions of Identity By Descent (IBD) in inbred families, by visually presenting colour-coded SNP genotype data ordered by physical or genetic distance.

::DEVELOPER

Ian’s DNA@Leeds

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0

:: DOWNLOAD

 AutoSNPa

:: MORE INFORMATION

Citation

Hum Mutat. 2006 Oct;27(10):1041-6.
Interactive visual analysis of SNP data for rapid autozygosity mapping in consanguineous families.
Carr IM, Flintoff KJ, Taylor GR, Markham AF, Bonthron DT.

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