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Items: 1 to 20 of 104

1.

Common workflow language (CWL)-based software pipeline for de novo genome assembly from long- and short-read data.

Korhonen PK, Hall RS, Young ND, Gasser RB.

Gigascience. 2019 Apr 1;8(4). pii: giz014. doi: 10.1093/gigascience/giz014.

2.

Software for pre-processing Illumina next-generation sequencing short read sequences.

Chen C, Khaleel SS, Huang H, Wu CH.

Source Code Biol Med. 2014 May 3;9:8. doi: 10.1186/1751-0473-9-8. eCollection 2014.

3.

HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly.

Huang S, Kang M, Xu A.

Bioinformatics. 2017 Aug 15;33(16):2577-2579. doi: 10.1093/bioinformatics/btx220.

4.

Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology.

English AC, Richards S, Han Y, Wang M, Vee V, Qu J, Qin X, Muzny DM, Reid JG, Worley KC, Gibbs RA.

PLoS One. 2012;7(11):e47768. doi: 10.1371/journal.pone.0047768. Epub 2012 Nov 21.

5.

SMRT sequencing only de novo assembly of the sugar beet (Beta vulgaris) chloroplast genome.

Stadermann KB, Weisshaar B, Holtgräwe D.

BMC Bioinformatics. 2015 Sep 16;16:295. doi: 10.1186/s12859-015-0726-6.

6.

MinION-based long-read sequencing and assembly extends the Caenorhabditis elegans reference genome.

Tyson JR, O'Neil NJ, Jain M, Olsen HE, Hieter P, Snutch TP.

Genome Res. 2018 Feb;28(2):266-274. doi: 10.1101/gr.221184.117. Epub 2017 Dec 22.

7.

Identification of optimum sequencing depth especially for de novo genome assembly of small genomes using next generation sequencing data.

Desai A, Marwah VS, Yadav A, Jha V, Dhaygude K, Bangar U, Kulkarni V, Jere A.

PLoS One. 2013 Apr 12;8(4):e60204. doi: 10.1371/journal.pone.0060204. Print 2013.

8.

A pipeline for local assembly of minisatellite alleles from single-molecule sequencing data.

Ogeh D, Badge R.

Bioinformatics. 2017 Mar 1;33(5):650-653. doi: 10.1093/bioinformatics/btw687.

9.

Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies.

Roach MJ, Schmidt SA, Borneman AR.

BMC Bioinformatics. 2018 Nov 29;19(1):460. doi: 10.1186/s12859-018-2485-7.

10.

An integrated pipeline for de novo assembly of microbial genomes.

Tritt A, Eisen JA, Facciotti MT, Darling AE.

PLoS One. 2012;7(9):e42304. doi: 10.1371/journal.pone.0042304. Epub 2012 Sep 13.

11.

A graph-based approach to diploid genome assembly.

Garg S, Rautiainen M, Novak AM, Garrison E, Durbin R, Marschall T.

Bioinformatics. 2018 Jul 1;34(13):i105-i114. doi: 10.1093/bioinformatics/bty279.

12.

SnpFilt: A pipeline for reference-free assembly-based identification of SNPs in bacterial genomes.

Chan CHS, Octavia S, Sintchenko V, Lan R.

Comput Biol Chem. 2016 Dec;65:178-184. doi: 10.1016/j.compbiolchem.2016.09.004. Epub 2016 Sep 9.

PMID:
27647159
13.

De novo assembly of Dekkera bruxellensis: a multi technology approach using short and long-read sequencing and optical mapping.

Olsen RA, Bunikis I, Tiukova I, Holmberg K, Lötstedt B, Pettersson OV, Passoth V, Käller M, Vezzi F.

Gigascience. 2015 Nov 26;4:56. doi: 10.1186/s13742-015-0094-1. eCollection 2015.

14.

Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data.

Page AJ, De Silva N, Hunt M, Quail MA, Parkhill J, Harris SR, Otto TD, Keane JA.

Microb Genom. 2016 Aug 25;2(8):e000083. doi: 10.1099/mgen.0.000083. eCollection 2016 Aug.

15.

PacBio But Not Illumina Technology Can Achieve Fast, Accurate and Complete Closure of the High GC, Complex Burkholderia pseudomallei Two-Chromosome Genome.

Teng JLL, Yeung ML, Chan E, Jia L, Lin CH, Huang Y, Tse H, Wong SSY, Sham PC, Lau SKP, Woo PCY.

Front Microbiol. 2017 Aug 2;8:1448. doi: 10.3389/fmicb.2017.01448. eCollection 2017.

16.

Organelle_PBA, a pipeline for assembling chloroplast and mitochondrial genomes from PacBio DNA sequencing data.

Soorni A, Haak D, Zaitlin D, Bombarely A.

BMC Genomics. 2017 Jan 7;18(1):49. doi: 10.1186/s12864-016-3412-9.

17.

CloudNeo: a cloud pipeline for identifying patient-specific tumor neoantigens.

Bais P, Namburi S, Gatti DM, Zhang X, Chuang JH.

Bioinformatics. 2017 Oct 1;33(19):3110-3112. doi: 10.1093/bioinformatics/btx375.

18.

De novo assembly of middle-sized genome using MinION and Illumina sequencers.

Minei R, Hoshina R, Ogura A.

BMC Genomics. 2018 Sep 24;19(1):700. doi: 10.1186/s12864-018-5067-1.

19.

Fusobacterium Genomics Using MinION and Illumina Sequencing Enables Genome Completion and Correction.

Todd SM, Settlage RE, Lahmers KK, Slade DJ.

mSphere. 2018 Jul 5;3(4). pii: e00269-18. doi: 10.1128/mSphere.00269-18.

20.

SQUAT: a Sequencing Quality Assessment Tool for data quality assessments of genome assemblies.

Yang LA, Chang YJ, Chen SH, Lin CY, Ho JM.

BMC Genomics. 2019 Apr 18;19(Suppl 9):238. doi: 10.1186/s12864-019-5445-3.

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