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Items: 1 to 20 of 167

1.

gSearch: a fast and flexible general search tool for whole-genome sequencing.

Song T, Hwang KB, Hsing M, Lee K, Bohn J, Kong SW.

Bioinformatics. 2012 Aug 15;28(16):2176-7. doi: 10.1093/bioinformatics/bts358. Epub 2012 Jun 23.

2.

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.

Wang K, Li M, Hakonarson H.

Nucleic Acids Res. 2010 Sep;38(16):e164. doi: 10.1093/nar/gkq603. Epub 2010 Jul 3.

3.

WhopGenome: high-speed access to whole-genome variation and sequence data in R.

Wittelsbürger U, Pfeifer B, Lercher MJ.

Bioinformatics. 2015 Feb 1;31(3):413-5. doi: 10.1093/bioinformatics/btu636. Epub 2014 Oct 1.

PMID:
25273104
4.

VCF-Miner: GUI-based application for mining variants and annotations stored in VCF files.

Hart SN, Duffy P, Quest DJ, Hossain A, Meiners MA, Kocher JP.

Brief Bioinform. 2016 Mar;17(2):346-51. doi: 10.1093/bib/bbv051. Epub 2015 Jul 25.

5.

The variant call format and VCFtools.

Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R; 1000 Genomes Project Analysis Group.

Bioinformatics. 2011 Aug 1;27(15):2156-8. doi: 10.1093/bioinformatics/btr330. Epub 2011 Jun 7.

6.

BEDTools: a flexible suite of utilities for comparing genomic features.

Quinlan AR, Hall IM.

Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28.

7.

Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant tools.

San Lucas FA, Wang G, Scheet P, Peng B.

Bioinformatics. 2012 Feb 1;28(3):421-2. doi: 10.1093/bioinformatics/btr667. Epub 2011 Dec 2.

8.

Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR.

Yang H, Wang K.

Nat Protoc. 2015 Oct;10(10):1556-66. doi: 10.1038/nprot.2015.105. Epub 2015 Sep 17.

9.

CrossMap: a versatile tool for coordinate conversion between genome assemblies.

Zhao H, Sun Z, Wang J, Huang H, Kocher JP, Wang L.

Bioinformatics. 2014 Apr 1;30(7):1006-7. doi: 10.1093/bioinformatics/btt730. Epub 2013 Dec 18.

10.

Jannovar: a java library for exome annotation.

Jäger M, Wang K, Bauer S, Smedley D, Krawitz P, Robinson PN.

Hum Mutat. 2014 May;35(5):548-55. doi: 10.1002/humu.22531. Epub 2014 Apr 9.

PMID:
24677618
11.

An Efficient Search Algorithm for Finding Genomic-Range Overlaps Based on the Maximum Range Length.

Seok HS, Song T, Kong SW, Hwang KB.

IEEE/ACM Trans Comput Biol Bioinform. 2015 Jul-Aug;12(4):778-84. doi: 10.1109/TCBB.2014.2369042.

PMID:
26357316
12.

The personal genome browser: visualizing functions of genetic variants.

Juan L, Teng M, Zang T, Hao Y, Wang Z, Yan C, Liu Y, Li J, Zhang T, Wang Y.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W192-7. doi: 10.1093/nar/gku361. Epub 2014 May 5.

13.

Prokka: rapid prokaryotic genome annotation.

Seemann T.

Bioinformatics. 2014 Jul 15;30(14):2068-9. doi: 10.1093/bioinformatics/btu153. Epub 2014 Mar 18.

14.

Vcfanno: fast, flexible annotation of genetic variants.

Pedersen BS, Layer RM, Quinlan AR.

Genome Biol. 2016 Jun 1;17(1):118. doi: 10.1186/s13059-016-0973-5.

15.

BrowseVCF: a web-based application and workflow to quickly prioritize disease-causative variants in VCF files.

Salatino S, Ramraj V.

Brief Bioinform. 2016 Jul 3. pii: bbw054. [Epub ahead of print]

PMID:
27373737
16.

MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing.

Calabrese C, Simone D, Diroma MA, Santorsola M, Guttà C, Gasparre G, Picardi E, Pesole G, Attimonelli M.

Bioinformatics. 2014 Nov 1;30(21):3115-7. doi: 10.1093/bioinformatics/btu483. Epub 2014 Jul 14.

17.

GFF-Ex: a genome feature extraction package.

Rastogi A, Gupta D.

BMC Res Notes. 2014 May 24;7:315. doi: 10.1186/1756-0500-7-315.

18.

Variant Calling From Next Generation Sequence Data.

Hansen NF.

Methods Mol Biol. 2016;1418:209-24. doi: 10.1007/978-1-4939-3578-9_11.

PMID:
27008017
19.

SeqAnt: a web service to rapidly identify and annotate DNA sequence variations.

Shetty AC, Athri P, Mondal K, Horner VL, Steinberg KM, Patel V, Caspary T, Cutler DJ, Zwick ME.

BMC Bioinformatics. 2010 Sep 20;11:471. doi: 10.1186/1471-2105-11-471.

20.

The UCSC genome browser and associated tools.

Kuhn RM, Haussler D, Kent WJ.

Brief Bioinform. 2013 Mar;14(2):144-61. doi: 10.1093/bib/bbs038. Epub 2012 Aug 20.

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