MakeHub 1.0.5 – Fully Automated Generation of UCSC Assembly Hubs

MakeHub 1.0.5

:: DESCRIPTION

MakeHub is a command line tool for the fully automatic generation of of track data hubs for visualizing genomes with the UCSC genome browser. Track data hubs are data structures that contain all required information about a genome for visualizing with the UCSC genome browser.

::DEVELOPER

Bioinformatics Greifswald

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

MakeHub

:: MORE INFORMATION

Citation

Hoff KJ.
MakeHub: Fully Automated Generation of UCSC Genome Browser Assembly Hubs.
Genomics Proteomics Bioinformatics. 2019 Oct;17(5):546-549. doi: 10.1016/j.gpb.2019.05.003. Epub 2020 Jan 28. PMID: 32001327; PMCID: PMC7056914.

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.

SvABA 1.1.0 – Structural Variation and Indel Detection by local Assembly

SvABA 1.1.0

:: DESCRIPTION

SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly.

::DEVELOPER

Jeremiah Wala (jwala@broadinstitute.org) — Rameen Berkoukhim lab — Dana Farber Cancer Institute, Boston, MA.

:: SCREENSHOTS

N/a

:: REQUIREMENTS

Linux

:: DOWNLOAD

SvABA

:: MORE INFORMATION

Citation

Wala JA, Bandopadhayay P, Greenwald NF, O’Rourke R, Sharpe T, Stewart C, Schumacher S, Li Y, Weischenfeldt J, Yao X, Nusbaum C, Campbell P, Getz G, Meyerson M, Zhang CZ, Imielinski M, Beroukhim R.
SvABA: genome-wide detection of structural variants and indels by local assembly.
Genome Res. 2018 Apr;28(4):581-591. doi: 10.1101/gr.221028.117. Epub 2018 Mar 13. PMID: 29535149; PMCID: PMC5880247.

XGenovo – Extended Genovo Metagenomic Assembler by Incorporating Paired-End Information

XGenovo

:: DESCRIPTION

XGenovo (Extended Genovo) is an extended genovo metagenomic assembler by incorporating paired-end information

::DEVELOPER

Sakakibara Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

XGenovo

:: MORE INFORMATION

Citation

Afiahayati, Sato K, Sakakibara Y. (2013)
An extended genovo metagenomic assembler by incorporating paired-end information.
PeerJ 1:e196

EWRA – Edge-Weighted Reconstruction integrating aDNA Assembly graph

EWRA

:: DESCRIPTION

The EWRA algorithm computes a parsimonious reconstruction of marker adjacencies minimizing the Single-Cut-or-Join (SCJ) distance along a given phylogenetic tree, including the information provided by an assembly graph of ancient DNA (aDNA) data at one internal node of the tree.

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

EWRA

:: MORE INFORMATION

Citation

Luhmann N, Chauve C, Stoye J, Wittler R.
Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework.
IEEE/ACM Trans Comput Biol Bioinform. 2018 Nov-Dec;15(6):2094-2100. doi: 10.1007/978-3-319-12418-6_17. Epub 2018 Mar 15. PMID: 29993816.

HASLR – Fast Hybrid Assembly of Long Reads

HASLR

:: DESCRIPTION

HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation Sequencing reads (such as Illumina) from the same sample

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

HASLR

:: MORE INFORMATION

Citation

Haghshenas E, Asghari H, Stoye J, Chauve C, Hach F.
HASLR: Fast Hybrid Assembly of Long Reads.
iScience. 2020 Aug 21;23(8):101389. doi: 10.1016/j.isci.2020.101389. Epub 2020 Jul 25. PMID: 32781410; PMCID: PMC7419660.

HyAsP – Hybrid Assembler for Plasmids

HyAsP

:: DESCRIPTION

HyAsP is a tool for the extracting plasmids from WGS assemblies in an automatic way. It combines ideas from both reference-based and depth-based methods to identify plasmids in a greedy algorithm, using information on the occurrences of known plasmid genes and considering characteristics of the contigs such as read depth and GC content.

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
conda

:: DOWNLOAD

HyAsP

:: MORE INFORMATION

Citation

Müller R, Chauve C.
HyAsP, a greedy tool for plasmids identification.
Bioinformatics. 2019 Nov 1;35(21):4436-4439. doi: 10.1093/bioinformatics/btz413. PMID: 31116364.

Binnacle – Using Scaffolds to Improve the Contiguity and Quality of Metagenomic Bins

Binnacle

:: DESCRIPTION

binnacle is a tool for binning metagenomic datasets using assembly graphs and scaffolds generated by metacarvel.

::DEVELOPER

MarBL (Maryland Bioinformatics Labs)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

binnacle

:: MORE INFORMATION

Citation

Muralidharan HS, Shah N, Meisel JS, Pop M.
Binnacle: Using Scaffolds to Improve the Contiguity and Quality of Metagenomic Bins.
Front Microbiol. 2021 Feb 24;12:638561. doi: 10.3389/fmicb.2021.638561. PMID: 33717033; PMCID: PMC7945042.

SALSA v2.3 – Scaffold long read Assemblies with Hi-C data

SALSA v2.3

:: DESCRIPTION

SALSA is a tool to scaffold long read assemblies with Hi-C.

::DEVELOPER

MarBL (Maryland Bioinformatics Labs)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

SALSA

:: MORE INFORMATION

Citation

Ghurye J, Pop M, Koren S, Bickhart D, Chin CS.
Scaffolding of long read assemblies using long range contact information.
BMC Genomics. 2017 Jul 12;18(1):527. doi: 10.1186/s12864-017-3879-z. PMID: 28701198; PMCID: PMC5508778.