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Items: 1 to 20 of 157

1.

Canary: an atomic pipeline for clinical amplicon assays.

Doig KD, Ellul J, Fellowes A, Thompson ER, Ryland G, Blombery P, Papenfuss AT, Fox SB.

BMC Bioinformatics. 2017 Dec 15;18(1):555. doi: 10.1186/s12859-017-1950-z.

2.

PathOS: a decision support system for reporting high throughput sequencing of cancers in clinical diagnostic laboratories.

Doig KD, Fellowes A, Bell AH, Seleznev A, Ma D, Ellul J, Li J, Doyle MA, Thompson ER, Kumar A, Lara L, Vedururu R, Reid G, Conway T, Papenfuss AT, Fox SB.

Genome Med. 2017 Apr 24;9(1):38. doi: 10.1186/s13073-017-0427-z.

3.

BigDataScript: a scripting language for data pipelines.

Cingolani P, Sladek R, Blanchette M.

Bioinformatics. 2015 Jan 1;31(1):10-6. doi: 10.1093/bioinformatics/btu595. Epub 2014 Sep 3.

4.

Validation of a Customized Bioinformatics Pipeline for a Clinical Next-Generation Sequencing Test Targeting Solid Tumor-Associated Variants.

Schneider T, Smith GH, Rossi MR, Hill CE, Zhang L.

J Mol Diagn. 2018 May;20(3):355-365. doi: 10.1016/j.jmoldx.2018.01.007. Epub 2018 Feb 19.

PMID:
29471113
5.

VarGenius executes cohort-level DNA-seq variant calling and annotation and allows to manage the resulting data through a PostgreSQL database.

Musacchia F, Ciolfi A, Mutarelli M, Bruselles A, Castello R, Pinelli M, Basu S, Banfi S, Casari G, Tartaglia M, Nigro V; TUDP.

BMC Bioinformatics. 2018 Dec 12;19(1):477. doi: 10.1186/s12859-018-2532-4.

6.

DNAscan: personal computer compatible NGS analysis, annotation and visualisation.

Iacoangeli A, Al Khleifat A, Sproviero W, Shatunov A, Jones AR, Morgan SL, Pittman A, Dobson RJ, Newhouse SJ, Al-Chalabi A.

BMC Bioinformatics. 2019 Apr 27;20(1):213. doi: 10.1186/s12859-019-2791-8.

7.

Variant Tool Chest: an improved tool to analyze and manipulate variant call format (VCF) files.

Ebbert MT, Wadsworth ME, Boehme KL, Hoyt KL, Sharp AR, O'Fallon BD, Kauwe JS, Ridge PG.

BMC Bioinformatics. 2014;15 Suppl 7:S12. doi: 10.1186/1471-2105-15-S7-S12. Epub 2014 May 28.

8.

Clinical Implementation and Validation of Automated Human Genome Variation Society (HGVS) Nomenclature System for Next-Generation Sequencing-Based Assays for Cancer.

Callenberg KM, Santana-Santos L, Chen L, Ernst WL, De Moura MB, Nikiforov YE, Nikiforova MN, Roy S.

J Mol Diagn. 2018 Sep;20(5):628-634. doi: 10.1016/j.jmoldx.2018.05.006. Epub 2018 Jun 21.

PMID:
29936258
9.

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.

10.

PipeCraft: Flexible open-source toolkit for bioinformatics analysis of custom high-throughput amplicon sequencing data.

Anslan S, Bahram M, Hiiesalu I, Tedersoo L.

Mol Ecol Resour. 2017 Nov;17(6):e234-e240. doi: 10.1111/1755-0998.12692. Epub 2017 Jun 21.

PMID:
28544559
11.

Bio-Docklets: virtualization containers for single-step execution of NGS pipelines.

Kim B, Ali T, Lijeron C, Afgan E, Krampis K.

Gigascience. 2017 Aug 1;6(8):1-7. doi: 10.1093/gigascience/gix048.

12.

TOGGLE: toolbox for generic NGS analyses.

Monat C, Tranchant-Dubreuil C, Kougbeadjo A, Farcy C, Ortega-Abboud E, Amanzougarene S, Ravel S, Agbessi M, Orjuela-Bouniol J, Summo M, Sabot F.

BMC Bioinformatics. 2015 Nov 9;16:374. doi: 10.1186/s12859-015-0795-6.

13.

Challenges in exome analysis by LifeScope and its alternative computational pipelines.

Pranckevičiene E, Rančelis T, Pranculis A, Kučinskas V.

BMC Res Notes. 2015 Sep 7;8:421. doi: 10.1186/s13104-015-1385-4.

14.

A community-based resource for automatic exome variant-calling and annotation in Mendelian disorders.

Mutarelli M, Marwah V, Rispoli R, Carrella D, Dharmalingam G, Oliva G, di Bernardo D.

BMC Genomics. 2014;15 Suppl 3:S5. doi: 10.1186/1471-2164-15-S3-S5. Epub 2014 May 6.

15.

htsint: a Python library for sequencing pipelines that combines data through gene set generation.

Richards AJ, Herrel A, Bonneaud C.

BMC Bioinformatics. 2015 Sep 24;16:307. doi: 10.1186/s12859-015-0729-3.

16.

Identification of missing variants by combining multiple analytic pipelines.

Ren Y, Reddy JS, Pottier C, Sarangi V, Tian S, Sinnwell JP, McDonnell SK, Biernacka JM, Carrasquillo MM, Ross OA, Ertekin-Taner N, Rademakers R, Hudson M, Mainzer LS, Asmann YW.

BMC Bioinformatics. 2018 Apr 16;19(1):139. doi: 10.1186/s12859-018-2151-0.

17.

Bicycle: a bioinformatics pipeline to analyze bisulfite sequencing data.

Graña O, López-Fernández H, Fdez-Riverola F, González Pisano D, Glez-Peña D.

Bioinformatics. 2018 Apr 15;34(8):1414-1415. doi: 10.1093/bioinformatics/btx778.

PMID:
29211825
18.

fqtools: an efficient software suite for modern FASTQ file manipulation.

Droop AP.

Bioinformatics. 2016 Jun 15;32(12):1883-4. doi: 10.1093/bioinformatics/btw088. Epub 2016 Feb 18.

19.

SLIM: a flexible web application for the reproducible processing of environmental DNA metabarcoding data.

Dufresne Y, Lejzerowicz F, Perret-Gentil LA, Pawlowski J, Cordier T.

BMC Bioinformatics. 2019 Feb 19;20(1):88. doi: 10.1186/s12859-019-2663-2.

20.

LongISLND: in silico sequencing of lengthy and noisy datatypes.

Lau B, Mohiyuddin M, Mu JC, Fang LT, Bani Asadi N, Dallett C, Lam HY.

Bioinformatics. 2016 Dec 15;32(24):3829-3832. Epub 2016 Sep 25.

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