Lighter 1.1.2 – Fast and Memory-efficient Sequencing Error Correction without Counting

Lighter 1.1.2

:: DESCRIPTION

Lighter is a kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.

::DEVELOPER

Li Song

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsx/Linux

:: DOWNLOAD

 Lighter

:: MORE INFORMATION

Citation

Genome Biol. 2014;15(11):509.
Lighter: fast and memory-efficient sequencing error correction without counting.
Song L, Florea L, Langmead B.

DSK 2.1.0 – K-mer Counting software

DSK 2.1.0

:: DESCRIPTION

DSK is a k-mer counting software, similar to Jellyfish. Jellyfish is very fast but limited to large-memory servers and k ≤ 32. In contrast, DSK supports large values of k, and runs with (almost-)arbitrarily low memory usage and reasonably low temporary disk usage. DSK can count k-mers of large Illumina datasets on laptops and desktop computers.

::DEVELOPER

Rayan CHIKHI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 DSK

:: MORE INFORMATION

Citation

DSK: k-mer counting with very low memory usage.
Rizk G, Lavenier D, Chikhi R.
Bioinformatics. 2013 Mar 1;29(5):652-3. doi: 10.1093/bioinformatics/btt020. Epub 2013 Jan 16.

QuantiFly v2 – Automated Drosophila Egg Counting

QuantiFly v2

:: DESCRIPTION

QuantiFly  is a software package for automating egg counting in Drosophila genetics research.

::DEVELOPER

The Wolfson Imaging Centre

:: SCREENSHOTS

QuantiFly

::REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 QuantiFly

:: MORE INFORMATION

Citation

QuantiFly: Robust Trainable Software for Automated Drosophila Egg Counting.
Waithe D, Rennert P, Brostow G, Piper MD.
PLoS One. 2015 May 18;10(5):e0127659. doi: 10.1371/journal.pone.0127659.

TMARKER v2.21692 – Cell Nuclei Counting and Staining Estimation

TMARKER v2.21692

:: DESCRIPTION

TMARKER assists in cell nuclei counting and staining estimation of pathological immunohistochemical TMA images and non-TMA images.

::DEVELOPER

NEXUS Personalized Health Technologies

:: SCREENSHOTS

TMARKER

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

  TMARKER

:: MORE INFORMATION

Citation

J Pathol Inform. 2013 Mar 30;4(Suppl):S2. doi: 10.4103/2153-3539.109804.
TMARKER: A free software toolkit for histopathological cell counting and staining estimation.
Schüffler PJ, Fuchs TJ, Ong CS, Wild PJ, Rupp NJ, Buhmann JM.

Rcount – Simple and Flexible RNA-Seq Read Counting

Rcount

:: DESCRIPTION

Rcount is a software for simple and flexible RNA-Seq read counting. Rcount allows the user to assign priorities to certain feature types (e.g. higher priority for protein-coding genes compared to rRNA- coding genes) or to add flanking regions.

::DEVELOPER

Ueli Grossniklaus’s group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX

:: DOWNLOAD

 Rcount

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Oct 15. pii: btu680.
Rcount: simple and flexible RNA-Seq read counting.
Schmid MW, Grossniklaus U

EggCounter 1.0 – Counting Mosquitoes’ Eggs in a Given Image

EggCounter 1.0

:: DESCRIPTION

Egg counter is a simple and automatic application for the detection and counting mosquitoes’ eggs in a given image. After the automatic analysis it is possible to change and edit the result and save the final result as an image.

::DEVELOPER

EggCounter team

:: SCREENSHOTS

Eggcounter

:: REQUIREMENTS

  • Linux/MacOsX / Windows
  • Java

:: DOWNLOAD

 EggCounter

:: MORE INFORMATION

Citation

Parasit Vectors. 2012 Jun 19;5:122. doi: 10.1186/1756-3305-5-122.
A user-friendly software to easily count Anopheles egg batches.
Mollahosseini A, Rossignol M, Pennetier C, Cohuet A, Anjos AD, Chandre F, Shahbazkia HR.

MicroCounter 1.00 – automatic Counting of Objects such as Bacterial Colonies from an JPEG Image

MicroCounter 1.00

:: DESCRIPTION

MicroCounter is a tool for automatic counting of objects such as bacterial colonies from an JPEG image. Typical usage is counting bacteria from a an image taken from a microscope.

::DEVELOPER

Leonid Asipov 

:: SCREENSHOTS

MicroCounter

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 MicroCounter

:: MORE INFORMATION

MitoCounter 1.0.1 – Counting mitochondrial DNA Reads from Whole Genome Sequence

MitoCounter 1.0.1

:: DESCRIPTION

MitoCounter is a tool for counting mitochondrial DNA reads from Whole Genome Sequence

::DEVELOPER

Frank Hsueh-Ting Chu

:: SCREENSHOTS

MitoCounter

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 MitoCounter

:: MORE INFORMATION

Citation

BMC Genomics. 2012;13 Suppl 7:S5. doi: 10.1186/1471-2164-13-S7-S5. Epub 2012 Dec 13.
Quantitative assessment of mitochondrial DNA copies from whole genome sequencing.
Chu HT, Hsiao WW, Tsao TT, Chang CM, Liu YW, Fan CC, Lin H, Chang HH, Yeh TJ, Chen JC, Huang DM, Chen CC, Kao CY.

ColonyCount BETA – Assist Counting Bacterial Colonies on Agar Plates

ColonyCount BETA

:: DESCRIPTION

ColonyCount is a smartphone app that can assist when counting bacterial colonies on agar plates. Counting is done by taking a picture of plate and placing tags on colonies by tapping screen. ColonyCount will continuously attempt to automatically count remaining colonies using data from the manually placed tags. Region of interest can be defined by crop primitives and free-drawing exclusion areas. Besides counting the app can also be used to perform different measurements using line and sphere primitives.

::DEVELOPER

Toolbox Factory

:: SCREENSHOTS

ColonyCount

:: REQUIREMENTS

  • Android

:: DOWNLOAD

  ColonyCount

:: MORE INFORMATION

DeadEasy Mito-Glia – Counting of Mitotic Cells and Glial Cells in Drosophila

DeadEasy Mito-Glia

:: DESCRIPTION

DeadEasy Mito-Glia is an imageJ plug-in allows you to count automatically mitotic cells stained with PHistone3 in whole Drosophila embryos.

::DEVELOPER

Alicia Hidalgo lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 DeadEasy Mito-Glia

:: MORE INFORMATION

Citation

Forero MG, Learte AR, Cartwright S. and Hidalgo A. (2010)
DeadEasy Mito-Glia: automatic counting of mitotic cells and glial cells in Drosophila.
PLoS One 5(5): e10557. doi:10.1371/journal.pone.0010557.