Tag: Coverage

CONCOCT 1.1.0 – Clustering cONtigs with COverage and ComposiTion

CONCOCT 1.1.0

:: DESCRIPTION

CONCOCT is a program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.

::DEVELOPER

the Science for Life Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

CONCOCT

:: MORE INFORMATION

Citation

Alneberg J, Bjarnason BS, de Bruijn I, Schirmer M, Quick J, Ijaz UZ, Lahti L, Loman NJ, Andersson AF, Quince C.
Binning metagenomic contigs by coverage and composition.
Nat Methods. 2014 Nov;11(11):1144-6. doi: 10.1038/nmeth.3103. Epub 2014 Sep 14. PMID: 25218180.

PACVr 0.9.4 – Plastome Assembly Coverage Visualization in R

PACVr 0.9.4

:: DESCRIPTION

PACVr visualizes the coverage depth of a complete plastid genome as well as the equality of its inverted repeat regions in relation to the circular, quadripartite genome structure and the location of individual genes.

::DEVELOPER

Michael Gruenstaeudl

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOs
  • R

:: DOWNLOAD

PACVr

:: MORE INFORMATION

Citation

Gruenstaeudl M, Jenke N.
PACVr: plastome assembly coverage visualization in R.
BMC Bioinformatics. 2020 May 24;21(1):207. doi: 10.1186/s12859-020-3475-0. PMID: 32448146; PMCID: PMC7245912.

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

Nonpareil 3.3.4 – Estimate Average Coverage and Generate Nonpareil Curves

Nonpareil 3.3.4

:: DESCRIPTION

Nonpareil estimates the coverage of a Whole Genome Shotgun metagenome and generate projections of sequencing efforts.

::DEVELOPER

Environmental Microbial Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Mac /  Linux

:: DOWNLOAD

 Nonpareil

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 1;30(5):629-35. doi: 10.1093/bioinformatics/btt584. Epub 2013 Oct 11.
Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets.
Rodriguez-R LM1, Konstantinidis KT

KATSURA 1.0.1 – KEGG Pathway Coverage & Expression Analysis

KATSURA 1.0.1

:: DESCRIPTION

Katsura tool is a free open source Java application designed to overlay gene expression data, comparative genomics data, or quantitative shotgun proteomics data onto metabolic pathways. Katsura uses data from the Kyoto Encyclopedia of Genes and Genomes (KEGG), Kanehisa Laboratory at Kyoto University, to build a small database containing KEGG pathway and enzyme data relating to one or more user specified organisms. Katsura manages the local database allowing users to update core information, add genomes of interest, backup the database and display database status reports. Gene expression data is input to allow visualization of pathway level expression trends over time or over a series of experimental conditions. A separate table visualizes the individual enzymes and associated gene expression values for each pathway. Capabilities such as bookmarking pathways to annotate findings, saving results to reloadable files, and the ability to output pdf reports and summary files help to capture key research findings.

::DEVELOPER

KATSURA team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • JAVA

:: DOWNLOAD

KATSURA

:: MORE INFORMATION

This application is released under the GPL v3 License: View License

Citation:

  1. Kanehisa, M., Goto, S., Furumichi, M., Tanabe, M., and Hirakawa, M.; KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res. 38, D355-D360 (2010).
  2. Kanehisa, M., Goto, S., Hattori, M., Aoki-Kinoshita, K.F., Itoh, M., Kawashima, S., Katayama, T., Araki, M., and Hirakawa, M.; From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 34, D354-357 (2006).
  3. Kanehisa, M. and Goto, S.; KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30 (2000).

Indexcov – Fast Coverage Quality Control for Whole-genome Sequencing

Indexcov

:: DESCRIPTION

Indexcov is an efficient estimator of whole-genome sequencing coverage to rapidly identify samples with aberrant coverage profiles, reveal large scale chromosomal anomalies, recognize potential batch effects, and infer the sex of a sample.

::DEVELOPER

The Quinlan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GO

:: DOWNLOAD

Indexcov

:: MORE INFORMATION

Citation:

Gigascience. 2017 Nov 1;6(11):1-6. doi: 10.1093/gigascience/gix090.
Indexcov: fast coverage quality control for whole-genome sequencing.
Pedersen BS1,2, Collins RL3,4,5, Talkowski ME3,6,4,5, Quinlan AR

MetaCon – Unsupervised Clustering of Metagenomic Contigs with Probabilistic k-mers Statistics and Coverage

MetaCon

:: DESCRIPTION

MetaCon is a novel tool for unsupervised metagenomic contig binning based on probabilistic k-mers statistics and coverage.

::DEVELOPER

Matteo Comin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

MetaCon

:: MORE INFORMATION

Citation

BMC Bioinformatics, 20 (Suppl 9), 367 2019 Nov 22
MetaCon: Unsupervised Clustering of Metagenomic Contigs With Probabilistic K-Mers Statistics and Coverage
Jia Qian, Matteo Comin

nCOP – Network-based Coverage of Mutational Profiles

nCOP

:: DESCRIPTION

nCOP (Network coverage of patients) uncovers cancer-relevant genes using mutational data in the context of protein interaction networks.

::DEVELOPER

Mona Singh

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

nCOP

:: MORE INFORMATION

Citation

Cell Syst. 2017 Sep 27;5(3):221-229.e4. doi: 10.1016/j.cels.2017.09.003.
Network-Based Coverage of Mutational Profiles Reveals Cancer Genes.
Hristov BH, Singh M.

CovEst 0.5.6 – Estimate coverage from NGS data without Assembly

CovEst 0.5.6

:: DESCRIPTION

CovEst estimates coverage and size of the genome from NGS data without assembly. It uses k-mer based statistics and works even with datasets with <1x coverage.

:: DEVELOPER

Computational Biology @ Comenius University in Bratislava

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

CovEst

:: MORE INFORMATION

JointSLM 0.1 – Detect Recurrent Copy Number Variations in Depth of Coverage data

JointSLM 0.1

:: DESCRIPTION

The JointSLM R package allows one to simultaneously analyse multiple Depth Of Coverage (DOC) genomic profiles.

::DEVELOPER

the Computational Biology research group in Florence

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX/Windows
  • R package

:: DOWNLOAD

  JointSLM

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2011 May;39(10):e65. doi: 10.1093/nar/gkr068. Epub 2011 Feb 14.
Detecting common copy number variants in high-throughput sequencing data by using JointSLM algorithm.
Magi A, Benelli M, Yoon S, Roviello F, Torricelli F.