PepNovo 20120423 – De novo Sequencing of low Precision MS/MS Data

PepNovo 20120423

:: DESCRIPTION

PepNovo is a de novo sequencing algorithm for MS/MS spectra. PepNovo accepts MS/MS spectra in the following formats: dta,mgf,mzxml. This version of PepNovo is optimized for ion-trap mass spectromtetry that uses CID fragmentation (charges 1-3, dominant b/y ladders).

::DEVELOPER

Ari Frank

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/windows

:: DOWNLOAD

 PepNovo

:: MORE INFORMATION

Citation:

Predicting Intensity Ranks of Peptide Fragment Ions
Frank, A.M.
J. Proteome Research, 8:2226-2240, 2009

DeNovo Pipeline 1.5 – Protein Identification by de novo Interpretation

DeNovo Pipeline 1.5

:: DESCRIPTION

DeNovo Pipeline performes protein identification by de novo interpretation by coupling the PepNovo software for sequencing and the Fasta tool for homology searching.

::DEVELOPER

pappso (Plate-forme d’analyses protéomiques de Paris Sud-Ouest)

:: SCREENSHOTS

denovo_pipeline

:: REQUIREMENTS

  • Windows/ MacOsX / Linux
  • Java

:: DOWNLOAD

 DeNovo Pipeline

:: MORE INFORMATION

EvalDNA v1.1 – Evaluation of De Novo Assemblies

EvalDNA v1.1

:: DESCRIPTION

EvalDNA uses machine-learning methods to integrate genome assembly quality metrics into a single comprehensive quality score.

::DEVELOPER

Maddy MacDonald

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

EvalDNA

:: MORE INFORMATION

Citation

MacDonald ML, Lee KH.
EvalDNA: a machine learning-based tool for the comprehensive evaluation of mammalian genome assembly quality.
BMC Bioinformatics. 2021 Nov 27;22(1):570. doi: 10.1186/s12859-021-04480-2. PMID: 34837948.

CStone – de novo Transcriptome Assembler

CStone

:: DESCRIPTION

CStone is a de novo assembler for RNA-Seq data that uses de Bruijn like graphs and annotates each contig produced with one of three graph classification levels indicating whether or not it can be guaranteed to be non chimeric.

::DEVELOPER

John Archer

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • JRE

:: DOWNLOAD

CStone

:: MORE INFORMATION

Citation

Linheiro R, Archer J.
CStone: A de novo transcriptome assembler for short-read data that identifies non-chimeric contigs based on underlying graph structure.
PLoS Comput Biol. 2021 Nov 23;17(11):e1009631. doi: 10.1371/journal.pcbi.1009631. Epub ahead of print. PMID: 34813594.

Edena v3.131028 – De Novo Short Reads Assembler

Edena v3.131028

:: DESCRIPTION

Edena is an assembler dedicated to process the millions of very short reads produced by the Illumina Genome Analyzer

::DEVELOPER

D. Hernandez @ The Genomic Research Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Edena

:: MORE INFORMATION

Citation:

Hernandez D, François P, Farinelli L, Osterås, Schrenzel J.
De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer.
Genome Research. 18:802-809, 2008.

PRICE 1.2 – de novo Genome Assembler

PRICE 1.2

:: DESCRIPTION

PRICE (Paired-Read Iterative Contig Extension) is a de novo genome assembler implemented in C++. Its name describes the strategy that it implements for genome assembly: PRICE uses paired-read information to iteratively increase the size of existing contigs. Initially, those contigs can be individual reads from a subset of the paired-read dataset, non-paired reads from sequencing technologies that provide non-paired data, or contigs that were output from a prior run of PRICE or any other assembler.

::DEVELOPER

DeRisi LabUCSF

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 PRICE

:: MORE INFORMATION

Citation

PRICE: Software for the Targeted Assembly of Components of (Meta)Genomic Sequence Data
J. Graham Ruby, Priya Bellare and Joseph L. DeRisi
G3 March 23, 2013 g3.113.005967

ABySS 2.3.2 – de novo, parallel, paired-end Sequence Assembler

ABySS 2.3.2

:: 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

Paulino D, Warren RL, Vandervalk BP, Raymond A, Jackman SD, Birol I.
Sealer: a scalable gap-closing application for finishing draft genomes.
BMC Bioinformatics. 2015 Jul 25;16(1):230. doi: 10.1186/s12859-015-0663-4. PMID: 26209068; PMCID: PMC4515008.

Vandervalk BP, Yang C, Xue Z, Raghavan K, Chu J, Mohamadi H, Jackman SD, Chiu R, Warren RL, Birol I.
Konnector v2.0: pseudo-long reads from paired-end sequencing data.
BMC Med Genomics. 2015;8 Suppl 3(Suppl 3):S1. doi: 10.1186/1755-8794-8-S3-S1. Epub 2015 Sep 23. PMID: 26399504; PMCID: PMC4582294.

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

fq2dna 21.06 – FASTQ files to de novo Assembly

fq2dna 21.06

:: DESCRIPTION

fq2dna is a command line tool to ease the de novo assembly of archaea, bacteria or virus genomes from raw high-throughput sequencing (HTS) paired-end (PE) reads.

::DEVELOPER

Alexis Criscuolo (alexis.criscuolo@pasteur.fr)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/  MacOsX

:: DOWNLOAD

fq2dna

:: MORE INFORMATION

HipMer 1.2.2 / MetaHipMer 2.0.1 – Extreme Scale De Novo Genome and MetaGenome Assembler

HipMer 1.2.2 / MetaHipMer 2.0.1

:: DESCRIPTION

HipMer is a high-performance application that produces high-quality de novo assemblies for very large-scale genomes.

The MetaHipMer extension is a recent addition to HipMer that is geared to large metagenomes and leverages iterative kmer sizes and a specialized scaffolding algorithm to produce increased contiguity and accuracy in metagenomic assemblies. It is able to reconstruct rRNA elements via a separate algorithm which relies on reference SSU and LSU Hidden Markov Models to help traverse the contig graph around ribosomal RNA regions.

::DEVELOPER

Berkeley Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

HipMer / MetaHipMer

:: MORE INFORMATION

Citation

E. Georganas et al.,
HipMer: an extreme-scale de novo genome assembler,
SC ’15: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, 2015, pp. 1-11, doi: 10.1145/2807591.2807664.

Hofmeyr S, Egan R, Georganas E, Copeland AC, Riley R, Clum A, Eloe-Fadrosh E, Roux S, Goltsman E, Buluç A, Rokhsar D, Oliker L, Yelick K.
Terabase-scale metagenome coassembly with MetaHipMer.
Sci Rep. 2020 Jul 1;10(1):10689. doi: 10.1038/s41598-020-67416-5. PMID: 32612216; PMCID: PMC7329831.

CisModule 20051205 – De novo Discovery of Cis-regulatory Modules

CisModule 20051205

:: DESCRIPTION

CisModule: A Bayesian module sampler by hierachical mixture modeling

::DEVELOPER

Qing Zhou

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX

:: DOWNLOAD

 CisModule

:: MORE INFORMATION

Citation

Zhou, Q. and Wong, W.H. (2004).
CisModule: De novo discovery of cis-regulatory modules by hierarchical mixture modeling.
Proceedings of the National Academy of Sciences USA, 101: 12114-12119.