Literature DB >> 31535074

GFAKluge: A C++ library and command line utilities for the Graphical Fragment Assembly formats.

Eric T Dawson1,2, Richard Durbin1.   

Abstract

SUMMARY: GFA has emerged as a standard format for the exchange of genome assemblies and sequence graphs. To encourage further adoption in high-performance software we have developed an open-source C++ library for GFA and a set of utilities for summarizing and manipulating the format. AVAILABILITY: The gfakluge source code is freely available under the MIT license at https://github.com/edawson/gfakluge. It has been tested on both Mac OS X and Linux.

Entities:  

Year:  2019        PMID： 31535074      PMCID： PMC6751074          DOI： 10.21105/joss.01083

Source DB:  PubMed          Journal:  J Open Source Softw        ISSN： 2475-9066


  5 in total

1.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs.

Authors:  Daniel R Zerbino; Ewan Birney
Journal:  Genome Res       Date:  2008-03-18       Impact factor: 9.043

2.  ABySS: a parallel assembler for short read sequence data.

Authors:  Jared T Simpson; Kim Wong; Shaun D Jackman; Jacqueline E Schein; Steven J M Jones; Inanç Birol
Journal:  Genome Res       Date:  2009-02-27       Impact factor: 9.043

3.  Efficient construction of an assembly string graph using the FM-index.

Authors:  Jared T Simpson; Richard Durbin
Journal:  Bioinformatics       Date:  2010-06-15       Impact factor: 6.937

4.  Bandage: interactive visualization of de novo genome assemblies.

Authors:  Ryan R Wick; Mark B Schultz; Justin Zobel; Kathryn E Holt
Journal:  Bioinformatics       Date:  2015-06-22       Impact factor: 6.937

5.  RGFA: powerful and convenient handling of assembly graphs.

Authors:  Giorgio Gonnella; Stefan Kurtz
Journal:  PeerJ       Date:  2016-11-08       Impact factor: 2.984
  5 in total
  2 in total

1.  The complete sequence of a human genome.

Authors:  Sergey Nurk; Sergey Koren; Arang Rhie; Mikko Rautiainen; Andrey V Bzikadze; Alla Mikheenko; Mitchell R Vollger; Nicolas Altemose; Lev Uralsky; Ariel Gershman; Sergey Aganezov; Savannah J Hoyt; Mark Diekhans; Glennis A Logsdon; Michael Alonge; Stylianos E Antonarakis; Matthew Borchers; Gerard G Bouffard; Shelise Y Brooks; Gina V Caldas; Nae-Chyun Chen; Haoyu Cheng; Chen-Shan Chin; William Chow; Leonardo G de Lima; Philip C Dishuck; Richard Durbin; Tatiana Dvorkina; Ian T Fiddes; Giulio Formenti; Robert S Fulton; Arkarachai Fungtammasan; Erik Garrison; Patrick G S Grady; Tina A Graves-Lindsay; Ira M Hall; Nancy F Hansen; Gabrielle A Hartley; Marina Haukness; Kerstin Howe; Michael W Hunkapiller; Chirag Jain; Miten Jain; Erich D Jarvis; Peter Kerpedjiev; Melanie Kirsche; Mikhail Kolmogorov; Jonas Korlach; Milinn Kremitzki; Heng Li; Valerie V Maduro; Tobias Marschall; Ann M McCartney; Jennifer McDaniel; Danny E Miller; James C Mullikin; Eugene W Myers; Nathan D Olson; Benedict Paten; Paul Peluso; Pavel A Pevzner; David Porubsky; Tamara Potapova; Evgeny I Rogaev; Jeffrey A Rosenfeld; Steven L Salzberg; Valerie A Schneider; Fritz J Sedlazeck; Kishwar Shafin; Colin J Shew; Alaina Shumate; Ying Sims; Arian F A Smit; Daniela C Soto; Ivan Sović; Jessica M Storer; Aaron Streets; Beth A Sullivan; Françoise Thibaud-Nissen; James Torrance; Justin Wagner; Brian P Walenz; Aaron Wenger; Jonathan M D Wood; Chunlin Xiao; Stephanie M Yan; Alice C Young; Samantha Zarate; Urvashi Surti; Rajiv C McCoy; Megan Y Dennis; Ivan A Alexandrov; Jennifer L Gerton; Rachel J O'Neill; Winston Timp; Justin M Zook; Michael C Schatz; Evan E Eichler; Karen H Miga; Adam M Phillippy
Journal:  Science       Date:  2022-03-31       Impact factor: 63.714

2.  Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs.

Authors:  Giulio Formenti; Linelle Abueg; Angelo Brajuka; Nadolina Brajuka; Cristóbal Gallardo-Alba; Alice Giani; Olivier Fedrigo; Erich D Jarvis
Journal:  Bioinformatics       Date:  2022-07-07       Impact factor: 6.931
  2 in total

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