VERSE v1.0.5 – Versatile and Efficient RNA-Seq Read Counting Tool

VERSE v1.0.5

:: DESCRIPTION

VERSE is designed for high-performance read summarization for next generation sequencing. VERSE is 50x faster than HTSeq when computing the same gene counts. It introduces a novel, hierarchical assignment scheme, which allows simultaneous quantification of multiple feature types or annotation levels without repeatedly assigning reads. There is also a set of parameters the user can use to fine-tune the assignment logic. VERSE can be readily incorporated into any existing RNA-Seq analysis pipelines.

::DEVELOPER

the Kim Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs

:: DOWNLOAD

VERSE 

:: MORE INFORMATION

Citation

Zhu, Q., Fisher, S.A., Shallcross, J., Kim, J. (Preprint).
VERSE: a versatile and efficient RNA-Seq read counting tool. bioRxiv 053306.
doi: http://dx.doi.org/10.1101/053306

DLTCount – Counting and Sampling Gene Family Histories

DLTCount

:: DESCRIPTION

DLTCount : Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer models

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

DLTCount

:: MORE INFORMATION

Citation

Chauve C, Ponty Y, Wallner M.
Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer models.
J Math Biol. 2020 Apr;80(5):1353-1388. doi: 10.1007/s00285-019-01465-x. Epub 2020 Feb 15. PMID: 32060618; PMCID: PMC7052048.

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

DSK 2.3.3 – K-mer Counting software

DSK 2.3.3

:: 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.

Alfred v0.2.3 – BAM Alignment Statistics, Feature Counting and Annotation

Alfred v0.2.3

:: DESCRIPTION

Alfred is an efficient and versatile command-line application that computes multi-sample quality control metrics in a read-group aware manner. Alfred supports read counting, feature annotation and haplotype-resolved consensus computation using multiple sequence alignments

::DEVELOPER

Tobias Rausch

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Alfred

:: MORE INFORMATION

Citation:

Rausch T, Hsi-Yang Fritz M, Korbel JO, Benes V.
Alfred: interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencing.
Bioinformatics. 2019 Jul 15;35(14):2489-2491. doi: 10.1093/bioinformatics/bty1007. PMID: 30520945; PMCID: PMC6612896.

TMARKER v2.158 – Cell Nuclei Counting and Staining Estimation

TMARKER v2.158

:: 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.

QuantiFly v2.0.35 – Automated Drosophila Egg Counting

QuantiFly v2.0.35

:: DESCRIPTION

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

::DEVELOPER

Dominic Waithe

:: 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.

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.

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.