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Items: 1 to 20 of 261

1.

IgSimulator: a versatile immunosequencing simulator.

Safonova Y, Lapidus A, Lill J.

Bioinformatics. 2015 Oct 1;31(19):3213-5. doi: 10.1093/bioinformatics/btv326. Epub 2015 May 25.

PMID:
26007226
2.

IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis.

Safonova Y, Bonissone S, Kurpilyansky E, Starostina E, Lapidus A, Stinson J, DePalatis L, Sandoval W, Lill J, Pevzner PA.

Bioinformatics. 2015 Jun 15;31(12):i53-61. doi: 10.1093/bioinformatics/btv238.

3.

ACE: accurate correction of errors using K-mer tries.

Sheikhizadeh S, de Ridder D.

Bioinformatics. 2015 Oct 1;31(19):3216-8. doi: 10.1093/bioinformatics/btv332. Epub 2015 May 28.

PMID:
26026137
4.

Simulating Next-Generation Sequencing Datasets from Empirical Mutation and Sequencing Models.

Stephens ZD, Hudson ME, Mainzer LS, Taschuk M, Weber MR, Iyer RK.

PLoS One. 2016 Nov 28;11(11):e0167047. doi: 10.1371/journal.pone.0167047. eCollection 2016.

5.

BFC: correcting Illumina sequencing errors.

Li H.

Bioinformatics. 2015 Sep 1;31(17):2885-7. doi: 10.1093/bioinformatics/btv290. Epub 2015 May 6.

6.

IMSEQ--a fast and error aware approach to immunogenetic sequence analysis.

Kuchenbecker L, Nienen M, Hecht J, Neumann AU, Babel N, Reinert K, Robinson PN.

Bioinformatics. 2015 Sep 15;31(18):2963-71. doi: 10.1093/bioinformatics/btv309. Epub 2015 May 18.

PMID:
25987567
7.

SAGE2: parallel human genome assembly.

Molnar M, Haghshenas E, Ilie L.

Bioinformatics. 2018 Feb 15;34(4):678-680. doi: 10.1093/bioinformatics/btx648.

PMID:
29045591
8.

FinisherSC: a repeat-aware tool for upgrading de novo assembly using long reads.

Lam KK, LaButti K, Khalak A, Tse D.

Bioinformatics. 2015 Oct 1;31(19):3207-9. doi: 10.1093/bioinformatics/btv280. Epub 2015 Jun 3.

PMID:
26040454
9.

piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing.

Han BW, Wang W, Zamore PD, Weng Z.

Bioinformatics. 2015 Feb 15;31(4):593-5. doi: 10.1093/bioinformatics/btu647. Epub 2014 Oct 17.

10.

E2FM: an encrypted and compressed full-text index for collections of genomic sequences.

Montecuollo F, Schmid G, Tagliaferri R.

Bioinformatics. 2017 Sep 15;33(18):2808-2817. doi: 10.1093/bioinformatics/btx313.

PMID:
28498928
11.

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.

12.

SimLoRD: Simulation of Long Read Data.

Stöcker BK, Köster J, Rahmann S.

Bioinformatics. 2016 Sep 1;32(17):2704-6. doi: 10.1093/bioinformatics/btw286. Epub 2016 May 10.

PMID:
27166244
13.

Determining the quality and complexity of next-generation sequencing data without a reference genome.

Anvar SY, Khachatryan L, Vermaat M, van Galen M, Pulyakhina I, Ariyurek Y, Kraaijeveld K, den Dunnen JT, de Knijff P, 't Hoen PA, Laros JF.

Genome Biol. 2014;15(12):555.

14.

Bandage: interactive visualization of de novo genome assemblies.

Wick RR, Schultz MB, Zobel J, Holt KE.

Bioinformatics. 2015 Oct 15;31(20):3350-2. doi: 10.1093/bioinformatics/btv383. Epub 2015 Jun 22.

15.

WGBSSuite: simulating whole-genome bisulphite sequencing data and benchmarking differential DNA methylation analysis tools.

Rackham OJ, Dellaportas P, Petretto E, Bottolo L.

Bioinformatics. 2015 Jul 15;31(14):2371-3. doi: 10.1093/bioinformatics/btv114. Epub 2015 Mar 15.

16.

Mosdepth: quick coverage calculation for genomes and exomes.

Pedersen BS, Quinlan AR.

Bioinformatics. 2018 Mar 1;34(5):867-868. doi: 10.1093/bioinformatics/btx699.

17.

damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets.

Marshall OJ, Brand AH.

Bioinformatics. 2015 Oct 15;31(20):3371-3. doi: 10.1093/bioinformatics/btv386. Epub 2015 Jun 25.

18.

miRCat2: accurate prediction of plant and animal microRNAs from next-generation sequencing datasets.

Paicu C, Mohorianu I, Stocks M, Xu P, Coince A, Billmeier M, Dalmay T, Moulton V, Moxon S.

Bioinformatics. 2017 Aug 15;33(16):2446-2454. doi: 10.1093/bioinformatics/btx210.

19.

ANAQUIN: a software toolkit for the analysis of spike-in controls for next generation sequencing.

Wong T, Deveson IW, Hardwick SA, Mercer TR.

Bioinformatics. 2017 Jun 1;33(11):1723-1724. doi: 10.1093/bioinformatics/btx038.

PMID:
28130232
20.

ploidyNGS: visually exploring ploidy with Next Generation Sequencing data.

Augusto Corrêa Dos Santos R, Goldman GH, Riaño-Pachón DM.

Bioinformatics. 2017 Aug 15;33(16):2575-2576. doi: 10.1093/bioinformatics/btx204.

PMID:
28383704

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