Ask
Search
My library
ORKG

ORKG Ask

Our mission is to organize scholarly knowledge and make it accessible to humans and machines.

About

About ORKG Ask
Report issue
Statistics
Contact

Legal

Terms of use
Data protection (sheet)
Imprint
Accessibility
License

Technical

We
open source
System status
Changelog
Frontend: v1.41.0
Backend: v1.13.4

We use cookies to provide a better user experience.

Data Protection

Additional file 1: of STRetch: detecting and discovering pathogenic short tandem repeat expansions

Harriet Dashnow (307545)
Monkol Lek (287026)
Belinda Phipson (738935)
Andreas Halman (5672897)
Simon Sadedin (3419006)
Andrew Lonsdale (650180)
Mark Davis (144230)
Phillipa Lamont (5672900)
Joshua Clayton (2470396)
Nigel Laing (3498833)
Daniel MacArthur (3577367)
Alicia Oshlack (25139)

Publication date

August 2018

DOI

10.6084/m9.figshare.6993029.v1

Abstract

Supplementary tables, figures and methods STRetch_additional_file_1. (PDF 1095 kb

Extracted data

Related items

Additional file 3: of USA300 Staphylococcus aureus persists on multiple body sites following an infection

Timothy Read (333405)
Robert Petit (6055523)
Zachary Yin (6055526)
Tuyaa Montgomery (6055529)
Moira McNulty (6055532)
Michael David (35198)

December 2018

Additional figures and tables. Table S1. agr frameshifts. Figure S1. Provenance of strains sequenced...

Additional file 1: of Global variation in bacterial strains that cause tuberculosis disease: a systematic review and meta-analysis

Kirsten Wiens (5722874)
Lauren Woyczynski (5907722)
Jorge Ledesma (5907725)
Jennifer Ross (5722856)
Roberto Zenteno-Cuevas (4966426)
Amador Goodridge (5907728)
Irfan Ullah (847820)
Barun Mathema (221268)
Joel Djoba Siawaya (5907731)
Molly Biehl (5722865)
Sarah Ray (5722868)
Natalia Bhattacharjee (5722883)
Nathaniel Henry (4753743)
Robert Reiner (375125)
Hmwe Kyu (3729022)
Christopher Murray (3413792)
Simon Hay (638995)

November 2018

Supplementary appendix. Document containing complete description of literature search strings and da...

Supplementary material and code availability

John Oketch (10762737)

February 2023

Code used to run STR genotyping software (GangSTR, HipSTR, STRetch, ExpansionHunter, and ExpansionHu...

Additional file 2 of Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences

Readman Chiu (41422)
Indhu-Shree Rajan-Babu (840006)
Jan M. Friedman (11252261)
Inanc Birol (11282022)

August 2021

Additional file 2. Supplementary Table S2. Software versions and parameters used in all analysis in ...

Additional file 1 of Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences

Readman Chiu (41422)
Indhu-Shree Rajan-Babu (840006)
Jan M. Friedman (11252261)
Inanc Birol (11282022)

August 2021

Additional file 1. Supplementary Figs. S1-S6 and Table S1. Supplementary benchmarking results

Additional file 1 of Group-based variant calling leveraging next-generation supercomputing for large-scale whole-genome sequencing studies

Kristopher Standish (3450338)
Tristan Carland (3450341)
Glenn Lockwood (3450353)
Wayne Pfeiffer (3450335)
Mahidhar Tatineni (3450332)
C Huang (3450326)
Sarah Lamberth (3450329)
Yauheniya Cherkas (3450344)
Carrie Brodmerkel (137250)
Ed Jaeger (3450350)
Lance Smith (3450347)
Gunaretnam Rajagopal (259110)
Mark Curran (3450356)
Nicholas Schork (332955)

September 2015

Supplemental material. PDF file containing supplemental figures and descriptions (PDF 5120 kb

Additional file 2 of Genome-wide sequencing as a first-tier screening test for short tandem repeat expansions

Indhu-Shree Rajan-Babu (840006)
Junran J. Peng (11252255)
Readman Chiu (41422)
Chenkai Li (1407223)
Arezoo Mohajeri (11252258)
Egor Dolzhenko (8159448)
Michael A. Eberle (8779022)
Inanc Birol (277074)
Jan M. Friedman (11252261)

August 2021

Additional file 2: Table S3: CAUSES exome sequence data summary. Table S4: Commands and parameters u...

Diagnostics of short tandem repeat expansion variants using massively parallel sequencing and componential tools

Leeuw, Rick H. de
Garnier, Dominique
Kroon, H.M.J.M.
Horlings, G.C.
Meijer, Emile de
Buermans, Henk
Engelen, B.G.M. van
Knijff, Peter de
Raz, Vered
Horlings, G.C.
Knijff, P. de

January 2019

Contains fulltext : 201792.pdf (publisher's version ) (Open Access

Additional file 1: of MUFFINN: cancer gene discovery via network analysis of somatic mutation data

Ara Cho (1736176)
Jung Shim (3418757)
Eiru Kim (707696)
Fran Supek (105927)
Ben Lehner (4828)
Insuk Lee (41276)

June 2016

Supplementary online information including supplementary Figures S1âS9 and supplementary Table S1....

Additional file 1: of Leveraging genetically simple traits to identify small-effect variants for complex phenotypes

K. Kemper (3511319)
M. Littlejohn (3511313)
T. Lopdell (3511301)
B. Hayes (3511316)
L. Bennett (3511307)
R. Williams (3511298)
X. Xu (771131)
P. Visscher (3511304)
M. Carrick (3511310)
M. Goddard (3486104)

November 2016

Supplementary Materials. This document contains supplementary Tables S1-S5 and supplementary Figures...

Additional file 1 of Genome-wide sequencing as a first-tier screening test for short tandem repeat expansions

Indhu-Shree Rajan-Babu (840006)
Junran J. Peng (11252255)
Readman Chiu (41422)
Chenkai Li (1407223)
Arezoo Mohajeri (11252258)
Egor Dolzhenko (8159448)
Michael A. Eberle (8779022)
Inanc Birol (277074)
Jan M. Friedman (11252261)

August 2021

Additional file 1: Table S1: Experimental repeat size data of the samples in the Coriell European Ge...

Additional file 1 of PanDelos: a dictionary-based method for pan-genome content discovery

Vincenzo Bonnici (475167)
Rosalba Giugno (46523)
Vincenzo Manca (6031928)

November 2018

Supplementary materials of PanDelos: a dictionary-based method for pan-genome content discovery. (PD...

Additional file 5: of Interpreting whole genome sequencing for investigating tuberculosis transmission: a systematic review

Hollie-Ann Hatherell (2588509)
Caroline Colijn (164960)
Helen Stagg (3480410)
Charlotte Jackson (565035)
Joanne Winter (3507035)
Ibrahim Abubakar (217017)

March 2016

Appendix E. Factors affecting the number of polymorphisms detected in sequences. (DOCX 18 kb

Additional file 1 of SQUID: transcriptomic structural variation detection from RNA-seq

Cong Ma (270846)
Mingfu Shao (5096474)
Carl Kingsford (70642)

April 2018

Additional Text, Table S1 with descriptions, Figures S1âS8 with descriptions. (PDF 2979 kb

Additional file 1 of Resolving repeat families with long reads

Philipp Bongartz (6687029)

May 2019

Contains additional figures, explanations and details about the algorithms, comparisons and data set...

Additional file 3: of USA300 Staphylococcus aureus persists on multiple body sites following an infection

Timothy Read (333405)
Robert Petit (6055523)
Zachary Yin (6055526)
Tuyaa Montgomery (6055529)
Moira McNulty (6055532)
Michael David (35198)

December 2018

Additional figures and tables. Table S1. agr frameshifts. Figure S1. Provenance of strains sequenced...

Additional file 1: of Global variation in bacterial strains that cause tuberculosis disease: a systematic review and meta-analysis

Kirsten Wiens (5722874)
Lauren Woyczynski (5907722)
Jorge Ledesma (5907725)
Jennifer Ross (5722856)
Roberto Zenteno-Cuevas (4966426)
Amador Goodridge (5907728)
Irfan Ullah (847820)
Barun Mathema (221268)
Joel Djoba Siawaya (5907731)
Molly Biehl (5722865)
Sarah Ray (5722868)
Natalia Bhattacharjee (5722883)
Nathaniel Henry (4753743)
Robert Reiner (375125)
Hmwe Kyu (3729022)
Christopher Murray (3413792)
Simon Hay (638995)

November 2018

Supplementary appendix. Document containing complete description of literature search strings and da...

Supplementary material and code availability

John Oketch (10762737)

February 2023

Code used to run STR genotyping software (GangSTR, HipSTR, STRetch, ExpansionHunter, and ExpansionHu...

Additional file 2 of Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences

Readman Chiu (41422)
Indhu-Shree Rajan-Babu (840006)
Jan M. Friedman (11252261)
Inanc Birol (11282022)

August 2021

Additional file 2. Supplementary Table S2. Software versions and parameters used in all analysis in ...

Additional file 1 of Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences

Readman Chiu (41422)
Indhu-Shree Rajan-Babu (840006)
Jan M. Friedman (11252261)
Inanc Birol (11282022)

August 2021

Additional file 1. Supplementary Figs. S1-S6 and Table S1. Supplementary benchmarking results

Additional file 1 of Group-based variant calling leveraging next-generation supercomputing for large-scale whole-genome sequencing studies

Kristopher Standish (3450338)
Tristan Carland (3450341)
Glenn Lockwood (3450353)
Wayne Pfeiffer (3450335)
Mahidhar Tatineni (3450332)
C Huang (3450326)
Sarah Lamberth (3450329)
Yauheniya Cherkas (3450344)
Carrie Brodmerkel (137250)
Ed Jaeger (3450350)
Lance Smith (3450347)
Gunaretnam Rajagopal (259110)
Mark Curran (3450356)
Nicholas Schork (332955)

September 2015

Supplemental material. PDF file containing supplemental figures and descriptions (PDF 5120 kb

Additional file 2 of Genome-wide sequencing as a first-tier screening test for short tandem repeat expansions

Indhu-Shree Rajan-Babu (840006)
Junran J. Peng (11252255)
Readman Chiu (41422)
Chenkai Li (1407223)
Arezoo Mohajeri (11252258)
Egor Dolzhenko (8159448)
Michael A. Eberle (8779022)
Inanc Birol (277074)
Jan M. Friedman (11252261)

August 2021

Additional file 2: Table S3: CAUSES exome sequence data summary. Table S4: Commands and parameters u...

Diagnostics of short tandem repeat expansion variants using massively parallel sequencing and componential tools

Leeuw, Rick H. de
Garnier, Dominique
Kroon, H.M.J.M.
Horlings, G.C.
Meijer, Emile de
Buermans, Henk
Engelen, B.G.M. van
Knijff, Peter de
Raz, Vered
Horlings, G.C.
Knijff, P. de

January 2019

Contains fulltext : 201792.pdf (publisher's version ) (Open Access

Additional file 1: of MUFFINN: cancer gene discovery via network analysis of somatic mutation data

Ara Cho (1736176)
Jung Shim (3418757)
Eiru Kim (707696)
Fran Supek (105927)
Ben Lehner (4828)
Insuk Lee (41276)

June 2016

Supplementary online information including supplementary Figures S1âS9 and supplementary Table S1....

Additional file 1: of Leveraging genetically simple traits to identify small-effect variants for complex phenotypes

K. Kemper (3511319)
M. Littlejohn (3511313)
T. Lopdell (3511301)
B. Hayes (3511316)
L. Bennett (3511307)
R. Williams (3511298)
X. Xu (771131)
P. Visscher (3511304)
M. Carrick (3511310)
M. Goddard (3486104)

November 2016

Supplementary Materials. This document contains supplementary Tables S1-S5 and supplementary Figures...

Additional file 1 of Genome-wide sequencing as a first-tier screening test for short tandem repeat expansions

Indhu-Shree Rajan-Babu (840006)
Junran J. Peng (11252255)
Readman Chiu (41422)
Chenkai Li (1407223)
Arezoo Mohajeri (11252258)
Egor Dolzhenko (8159448)
Michael A. Eberle (8779022)
Inanc Birol (277074)
Jan M. Friedman (11252261)

August 2021

Additional file 1: Table S1: Experimental repeat size data of the samples in the Coriell European Ge...

Additional file 1 of PanDelos: a dictionary-based method for pan-genome content discovery

Vincenzo Bonnici (475167)
Rosalba Giugno (46523)
Vincenzo Manca (6031928)

November 2018

Supplementary materials of PanDelos: a dictionary-based method for pan-genome content discovery. (PD...

Additional file 5: of Interpreting whole genome sequencing for investigating tuberculosis transmission: a systematic review

Hollie-Ann Hatherell (2588509)
Caroline Colijn (164960)
Helen Stagg (3480410)
Charlotte Jackson (565035)
Joanne Winter (3507035)
Ibrahim Abubakar (217017)

March 2016

Appendix E. Factors affecting the number of polymorphisms detected in sequences. (DOCX 18 kb

Additional file 1 of SQUID: transcriptomic structural variation detection from RNA-seq

Cong Ma (270846)
Mingfu Shao (5096474)
Carl Kingsford (70642)

April 2018

Additional Text, Table S1 with descriptions, Figures S1âS8 with descriptions. (PDF 2979 kb

Additional file 1 of Resolving repeat families with long reads

Philipp Bongartz (6687029)

May 2019

Contains additional figures, explanations and details about the algorithms, comparisons and data set...

Additional file 3: of USA300 Staphylococcus aureus persists on multiple body sites following an infection

Timothy Read (333405)
Robert Petit (6055523)
Zachary Yin (6055526)
Tuyaa Montgomery (6055529)
Moira McNulty (6055532)
Michael David (35198)

December 2018

Additional figures and tables. Table S1. agr frameshifts. Figure S1. Provenance of strains sequenced...

Additional file 1: of Global variation in bacterial strains that cause tuberculosis disease: a systematic review and meta-analysis

Kirsten Wiens (5722874)
Lauren Woyczynski (5907722)
Jorge Ledesma (5907725)
Jennifer Ross (5722856)
Roberto Zenteno-Cuevas (4966426)
Amador Goodridge (5907728)
Irfan Ullah (847820)
Barun Mathema (221268)
Joel Djoba Siawaya (5907731)
Molly Biehl (5722865)
Sarah Ray (5722868)
Natalia Bhattacharjee (5722883)
Nathaniel Henry (4753743)
Robert Reiner (375125)
Hmwe Kyu (3729022)
Christopher Murray (3413792)
Simon Hay (638995)

November 2018

Supplementary appendix. Document containing complete description of literature search strings and da...

Supplementary material and code availability

John Oketch (10762737)

February 2023

Code used to run STR genotyping software (GangSTR, HipSTR, STRetch, ExpansionHunter, and ExpansionHu...