NPLB 1.0.0 – Learn de novo Promoter Architectures from Genome-wide TSSs

NPLB 1.0.0

:: DESCRIPTION

NPLB is an efficient, organism-independent method for characterizing such diverse architectures directly from experimentally identified genome-wide TSSs, without relying on known promoter elements.

::DEVELOPER

NPLB team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Python

:: DOWNLOAD

 NPLB

:: MORE INFORMATION

Citation

No Promoter Left Behind (NPLB): learn de novo promoter architectures from genome-wide transcription start sites.
Mitra S, Narlikar L.
Bioinformatics. 2015 Nov 2. pii: btv645.

Famdenovo 0.1.1 – Calculating the probability of being de novo for a Genetic Mutation using family history data

Famdenovo 0.1.1

:: DESCRIPTION

Famdenovo is an algorithm that calculates the probability of de novo status in deleterious germline mutations using family history data.

::DEVELOPER

Statistical Bioinformatics Lab, The University of Texas M. D. Anderson Cancer Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /MacOsX
  • R package

:: DOWNLOAD

Famdenovo

:: MORE INFORMATION

Citation

Gao F, Pan X, Dodd-Eaton EB, Recio CV, Montierth MD, Bojadzieva J, Mai PL, Zelley K, Johnson VE, Braun D, Nichols KE, Garber JE, Savage SA, Strong LC, Wang W.
A pedigree-based prediction model identifies carriers of deleterious de novo mutations in families with Li-Fraumeni syndrome.
Genome Res. 2020 Aug;30(8):1170-1180. doi: 10.1101/gr.249599.119. Epub 2020 Aug 18. PMID: 32817165; PMCID: PMC7462073.

Anchor 0.3.1 – Post-processing Tools for de novo Assemblies

Anchor 0.3.1

:: DESCRIPTION

Anchor is a set of tools for making automated improvements to de novo assemblies.

Anchor currently includes two main modules:

– Correction of erroneous single-nucleotide variants and small indels
– Scaffold-filling by local re-assembly

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Anchor

:: MORE INFORMATION

ABySS 2.1.5 – de novo, parallel, paired-end Sequence Assembler

ABySS 2.1.5

:: DESCRIPTION

ABySS (Assembly By Short Sequences) is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX

:: DOWNLOAD

 ABySS

:: MORE INFORMATION

Citation

Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I.
ABySS: A parallel assembler for short read sequence data.
Genome Res. 2009. 19: 1117-1123

TBnovo – De novo Protein Sequencing by combining Top-down and Bottom-up Mass Spectrometry

TBnovo

:: DESCRIPTION

TBNovo is a de novo protein sequencing software tool which combines both top down and bottom up tandem mass spectra.

::DEVELOPER

Xiaowen Liu ,CCMS The Center for Computational Mass Spectrometry

:: REQUIREMENTS

  • Linux/Windows
  • JRE

:: DOWNLOAD

 TBnovo

:: MORE INFORMATION

Citation

J Proteome Res. 2014 Jul 3;13(7):3241-8. doi: 10.1021/pr401300m. Epub 2014 Jun 18.
De novo protein sequencing by combining top-down and bottom-up tandem mass spectra.
Liu X1, Dekker LJ, Wu S, Vanduijn MM, Luider TM, Tolić N, Kou Q, Dvorkin M, Alexandrova S, Vyatkina K, Paša-Tolić L, Pevzner PA.

BOSS – Predicting Biological System Objectives de novo from internal State Measurements

BOSS

:: DESCRIPTION

BOSS (Biological Objective Solution Search) is a novel method for the inference of an objective function of a biological system from its underlying network stoichiometry as well as experimentally-measured state variables.

::DEVELOPER

the Computational Systems Biology Laboratory, Department of Biomedical Engineering, University of Virginia.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • GAMS

:: DOWNLOAD

 BOSS

:: MORE INFORMATION

Citation:

Gianchandani, E.P., M.A. Oberhardt, A.P. Burgard, C.D. Maranas, and J.A. Papin. 2008.
Predicting biological system objectives de novo from internal state measurements.
BMC Bioinformatics, 9:43

isONclust 0.0.4 – de novo Clustering of long Transcript Reads into Genes

isONclust 0.0.4

:: DESCRIPTION

isONclust is a tool for clustering either PacBio Iso-Seq reads, or Oxford Nanopore reads into clusters, where each cluster represents all reads that came from a gene.

::DEVELOPER

Medvedev Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

isONclust

:: MORE INFORMATION

Citation

Kristoffer Sahlin, Paul Medvedev (2019)
De Novo Clustering of Long-Read Transcriptome Data Using a Greedy, Quality-Value Based Algorithm“,
RECOMB 2019

RepeatModeler 2.0.1 – de-novo Repeat Family Identification and Modeling package

RepeatModeler 2.0.1

:: DESCRIPTION

RepeatModeler is a de-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.

::DEVELOPER

RepeatModeler team – Institute for Systems Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 RepeatModeler

:: MORE INFORMATION

Citation

PLoS One, 13 (3), e0193588 2018 Mar 14 eCollection 2018
Superior Ab Initio Identification, Annotation and Characterisation of TEs and Segmental Duplications From Genome Assemblies
Lu Zeng , R Daniel Kortschak , Joy M Raison , Terry Bertozzi , David L Adelson

Quartz 0.2 – de novo Quality Score Compression tool

Quartz 0.2

:: DESCRIPTION

Quartz (QUAlity score Reduction at Terabyte scale) is an efficient de novo quality score compression tool based on traversing the k-mer landscape of NGS read datasets.

::DEVELOPER

Bonnie Berger 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Quartz

:: MORE INFORMATION

Citation:

Nat Biotechnol, 33 (3), 240-3 Mar 2015
Quality Score Compression Improves Genotyping Accuracy
Y William Yu, Deniz Yorukoglu , Jian Peng, Bonnie Berger

A5-miseq 20160825 – de novo Assembly & Analysis of Illumina Sequence data

A5-miseq 20160825

:: DESCRIPTION

de novo assembly & analysis of Illumina sequence data, including the A5 pipeline, A5-miseq, tools to evaluate assembly quality, and scripts to facilitate data submission to NCBI and the RAST annotation system

::DEVELOPER

The Darling Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 A5-miseq

:: MORE INFORMATION

Citation

A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data.
Coil D, Jospin G, Darling AE.
Bioinformatics. 2014 Oct 22. pii: btu661.