Tag: Genome

ntJoin v1.0.8 – Genome Assembly Scaffolder using minimizer Graphs

ntJoin v1.0.8

:: DESCRIPTION

ntJoin is an assembly-guided scaffolder which uses a lightweight, alignment-free mapping strategy in lieu of alignments to quickly contiguate a target assembly using one or more

::DEVELOPER

BC Cancer Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Python

:: DOWNLOAD

ntJoin

:: MORE INFORMATION

Citation

Coombe L, Nikolić V, Chu J, Birol I, Warren RL.
ntJoin: Fast and lightweight assembly-guided scaffolding using minimizer graphs.
Bioinformatics. 2020 Jun 1;36(12):3885-3887. doi: 10.1093/bioinformatics/btaa253. PMID: 32311025; PMCID: PMC7320612.

ProbeMatch – Rapid Alignment of Oligonucleotides to Genome

ProbeMatch

:: DESCRIPTION

ProbeMatch is a sequence alignment program designed for matching a large set of oligonucleotide sequences against a genome database using gapped alignments. Unlike existing tools such as ELAND and MAQ which only perform ungapped alignments allowing at most 2-3 mismatches, ProbeMatch generates both ungapped and gapped alignments allowing up to 3 errors including insertion, deletion, and mismatch.

::DEVELOPER

Jignesh M. Patel

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

 ProbeMatch

:: MORE INFORMATION

Citation:

Bioinformatics. 2009 Jun 1;25(11):1424-5. doi: 10.1093/bioinformatics/btp178. Epub 2009 Apr 7.
ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches.
Kim YJ1, Teletia N, Ruotti V, Maher CA, Chinnaiyan AM, Stewart R, Thomson JA, Patel JM.

Geptop 2.0 – Gene Essentiality Prediction tool for COMPLETE-GENOME based on Orthology and Phylogeny

Geptop 2.0

:: DESCRIPTION

Geptop is a webserver, which first provides a platform to detect essential gene sets over bacterial species, by comparing orthology and phylogeny of query protein sets with essential gene datasets determined experimentally (from DEG database).

::DEVELOPER

Microbe and Drug Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux
  • Python
  • BioPython

:: DOWNLOAD

 Geptop

:: MORE INFORMATION

Citation

Wen QF, Wei W, Guo FB.
Geptop 2.0: Accurately Select Essential Genes from the List of Protein-Coding Genes in Prokaryotic Genomes.
Methods Mol Biol. 2022;2377:423-430. doi: 10.1007/978-1-0716-1720-5_23. PMID: 34709630.

PLoS One. 2013 Aug 15;8(8):e72343. doi: 10.1371/journal.pone.0072343. eCollection 2013.
Geptop: a gene essentiality prediction tool for sequenced bacterial genomes based on orthology and phylogeny.
Wei W1, Ning LW, Ye YN, Guo FB.

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.

GQL – Using Genome Query Language to uncover Genetic Variation

GQL

:: DESCRIPTION

GQL (Genome Query Language) allows for the efficient querying of genomic fragment data to uncover evidence for variation in the sampled genomes.

::DEVELOPER

Christos Kozanitis

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • C++ Compiler

:: DOWNLOAD

 GQL

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 Jan 1;30(1):1-8. doi: 10.1093/bioinformatics/btt250. Epub 2013 Jun 10.
Using Genome Query Language to uncover genetic variation.
Kozanitis C1, Heiberg A, Varghese G, Bafna V.

AccNET V1.2 – Accessory Genome Constellation Network

AccNET V1.2

:: DESCRIPTION

AccNET is a Perl application that presents a new way to study the accessory genome of a given set of organisms.

:: DEVELOPER

irycis Bioinfo

:: REQUIREMENTS

  • Linux / Window
  • Perl

:: DOWNLOAD

AccNET

:: MORE INFORMATION

Citation

Lanza VF, Baquero F, de la Cruz F, Coque TM.
AcCNET (Accessory Genome Constellation Network): comparative genomics software for accessory genome analysis using bipartite networks.
Bioinformatics. 2017 Jan 15;33(2):283-285. doi: 10.1093/bioinformatics/btw601. Epub 2016 Sep 23. PMID: 27663497.

cis-X v1.5.0 – Search for Activating Regulatory Variants in the Tumor Genome

cis-X v1.5.0

:: DESCRIPTION

cis-X is a new computational method for the discovery of noncoding regulatory variants in individual cancer genomes that will cause cis-activation of target gene transcription.

::DEVELOPER

Zhang (Jinghui Zhang) Lab,St. Jude Children’s Research Hospital

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

cis-X

:: MORE INFORMATION

OMGS – Optical Map-Based Genome Scaffolding

OMGS

:: DESCRIPTION

OMGS is a fast genome scaffolding tool which takes advantage of one or multiple Bionano optical maps to accurately generate scaffolds.

::DEVELOPER

Weihua Pan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

OMGS

:: MORE INFORMATION

Citation

Pan W, Jiang T, Lonardi S.
OMGS: Optical Map-Based Genome Scaffolding.
J Comput Biol. 2020 Apr;27(4):519-533. doi: 10.1089/cmb.2019.0310. Epub 2019 Dec 3. PMID: 31794680.

Novo&Stitch – Genome Assembly Reconciliation tool based on Optical Map

Novo&Stitch

:: DESCRIPTION

Novo&Stitch is an assembly reconciliation tool which takes advantage of optical maps to accurately carry out assembly reconciliation.

::DEVELOPER

Weihua Pan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

Novo&Stitch

:: MORE INFORMATION

Citation

Pan W, Wanamaker SI, Ah-Fong AMV, Judelson HS, Lonardi S.
Novo&Stitch: accurate reconciliation of genome assemblies via optical maps.
Bioinformatics. 2018 Jul 1;34(13):i43-i51. doi: 10.1093/bioinformatics/bty255. PMID: 29949964; PMCID: PMC6022655.

simuG v1.0.0 – General-purpose Genome Simulator

simuG v1.0.0

:: DESCRIPTION

simuG is a simple, flexible, and powerful tool to simulate genome sequences with pre-defined or random genomic variants.

::DEVELOPER

Jia-Xing Yue

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

simuG

:: MORE INFORMATION

Citation

Yue JX, Liti G.
simuG: a general-purpose genome simulator.
Bioinformatics. 2019 Nov 1;35(21):4442-4444. doi: 10.1093/bioinformatics/btz424. PMID: 31116378; PMCID: PMC6821417.