Tag: Reference

Refgenie v0.12.1 / refgenieserver v0.7.0 – Reference Genome Resource Manager

Refgenie v0.12.1 / refgenieserver v0.7.0

:: DESCRIPTION

Refgenie manages storage, access, and transfer of reference genome resources.

Refgenieserver is containerized code that hosts genome assets that can be automatically downloaded by the refgenie command-line interface.

::DEVELOPER

Sheffield lab of computational biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

Refgenie / Refgenieserver

:: MORE INFORMATION

Citation

Stolarczyk M, Reuter VP, Smith JP, Magee NE, Sheffield NC.
Refgenie: a reference genome resource manager.
Gigascience. 2020 Feb 1;9(2):giz149. doi: 10.1093/gigascience/giz149. PMID: 31995185; PMCID: PMC6988606.

DNAcompact 20130829 – Genome Compression algorithm with/without Reference

DNAcompact 20130829

:: DESCRIPTION

DNA-COMPACT is a software of DNA COMpression based on a pattern-aware contextual modeling technique.

::DEVELOPER

DNAcompact team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 DNAcompact

:: MORE INFORMATION

Citation

PLoS One. 2013 Nov 25;8(11):e80377. doi: 10.1371/journal.pone.0080377. eCollection 2013.
DNA-COMPACT: DNA COMpression based on a pattern-aware contextual modeling technique.
Li P1, Wang S, Kim J, Xiong H, Ohno-Machado L, Jiang X.

RefCov 0.3 – Analyzing Coverage of Sequence data across a Reference

RefCov 0.3

:: DESCRIPTION

The RefCov software suite was written as a toolkit to provide multiple methods for analyzing coverage of sequence data across a reference. As such, it does not answer a single question, but rather provides the ability to formulate and answer multiple analytical questions.

::DEVELOPER

The Genome Institute at Washington University School of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C compiler

:: DOWNLOAD

  RefCov

:: MORE INFORMATION

SeqCons 2.0.9 – de novo and reference-guided Sequence Assembly

SeqCons 2.0.9

:: DESCRIPTION

 SeqCons (Sequence consensus) is an open source consensus computation program for Linux and Windows. The algorithm can be used for de novo and reference-guided sequence assembly.

::DEVELOPER

SeqCons Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 SeqCons

:: MORE INFORMATION

Citation

Rausch, T., Koren, S., Gennady, D., Weese, D., Emde, A.-K., D?ring, A., Reinert, K. (2009).
A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads.
Bioinformatics (2009) 25 (9): 1118-1124.

RAREVATOR – RAre REference VAriant annotaTOR

RAREVATOR

:: DESCRIPTION

RAREVATOR is a tool for the identification and annotation of germline and somatic variants in rare reference allele loci from second generation sequencing data.

::DEVELOPER

RAREVATOR team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RAREVATOR

:: MORE INFORMATION

Citation:

Characterization and identification of hidden rare variants in the human genome
Magi A, D’Aurizio R, Palombo F, Cifola I, Tattini L, Semeraro R, Pippucci T, Giusti B, Romeo G, Abbate R, Gensini GF.
BMC Genomics. 2015 Apr 24;16(1):340.

Ragout 2.3 – Tool for Reference-assisted Assembly

Ragout 2.3

:: DESCRIPTION

Ragout (Reference-Assisted Genome Ordering UTility) is a tool for assisted assembly using multiple references. It takes a short read assembly (a set of contigs), a set of related references and a corresponding phylogenetic tree and then assembles the contigs into scaffolds.

::DEVELOPER

Mikhail Kolmogorov

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX / Windows
  • Python

:: DOWNLOAD

 Ragout

:: MORE INFORMATION

Citation

Ragout-a reference-assisted assembly tool for bacterial genomes.
Kolmogorov M, Raney B, Paten B, Pham S.
Bioinformatics. 2014 Jun 15;30(12):i302-i309. doi: 10.1093/bioinformatics/btu280.

misFinder v0.4.05.05 – Identify Mis-assemblies in an unbiased manner using Reference and Paired-end Reads

misFinder v0.4.05.05

:: DESCRIPTION

misFinder is a tool that aims to identify the assembly errors with high accuracy in an unbiased way and correct these errors at their mis-assembled positions to improve the assembly accuracy for downstream analysis.

::DEVELOPER

misFinder team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 misFinder

:: MORE INFORMATION

Citation

misFinder: identify mis-assemblies in an unbiased manner using reference and paired-end reads.
Zhu X, Leung HC, Wang R, Chin FY, Yiu SM, Quan G, Li Y, Zhang R, Jiang Q, Liu B, Dong Y, Zhou G, Wang Y.
BMC Bioinformatics. 2015 Nov 16;16(1):386.

HARSH 0.21 – Haplotype Inference using Reference and Sequencing Data

HARSH 0.21

:: DESCRIPTION

HARSH (HAplotype inference using Reference and Sequencing tecHnology) is a method to infer the haplotype using haplotype reference panel and high throughput sequencing data. It is based on a novel probabilistic model and Gibbs sampler method.

::DEVELOPER

ZarLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Python

:: DOWNLOAD

 HARSH

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Sep 15;29(18):2245-52. doi: 10.1093/bioinformatics/btt386.
Leveraging reads that span multiple single nucleotide polymorphisms for haplotype inference from sequencing data.
Yang WY, Hormozdiari F, Wang Z, He D, Pasaniuc B, Eskin E.

SHEAR 1.1.2 – Sample Heterogeneity Estimation and Assembly by Reference

SHEAR 1.1.2

:: DESCRIPTION

SHEAR is a tool for next-generation sequencing data analysis that predicts SVs, accounts for heterogeneous variants by estimating their representative percentages, and generates personal genomic sequences to be used for downstream analysis.

::DEVELOPER

Hwang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 SHEAR

:: MORE INFORMATION

Citation

BMC Genomics. 2014 Jan 29;15:84. doi: 10.1186/1471-2164-15-84.
SHEAR: sample heterogeneity estimation and assembly by reference.
Landman SR, Hwang TH1, Silverstein KA, Li Y, Dehm SM, Steinbach M, Kumar V.

MAXIMUS 0.2 – Hybrid Reference and de novo Assembly pipeline

MAXIMUS 0.2

:: DESCRIPTION

MAXIMUS is a genome assembly pipeline which takes the best out of multiple reference assemblies and de novo assembly. The benefits of this approach include better assembled repetitive regions, less gaps and higher accuracy for the resultant assembly.

::DEVELOPER

The Chinese University of Hong Kong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  MAXIMUS

:: MORE INFORMATION

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