Gapcloser

Manufactured by Illumina

Gapcloser is a laboratory instrument developed by Illumina for the purpose of closing sequence gaps in genetic data. The core function of Gapcloser is to facilitate the completion of DNA sequence assemblies by identifying and resolving regions of missing or uncertain sequence information.

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Lab products found in correlation

Genome analyzer iix gaiix, by Illumina (1 mentions) Pbjelly2, by Illumina (1 mentions) Pe reads, by Illumina (1 mentions) Solve v3.0.1, by Bionano Genomics (1 mentions)

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GapCloser software56

4 protocols using gapcloser

Scaffolding and Gap Filling for Genome Assembly

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The final Illumina assembly was further scaffolded with PacBio long reads using SSPACE‐LR (LongReads) (Boetzer and Pirovano, 2014) for scaffolding, followed by GAPCloser using Illumina reads and finally gap filled with PBJelly2 (English et al., 2012) using PacBio long reads.
The assembly generated from SSPACE‐LR was gap filled with GAPCloser (Illumina Data) and PBJelly2 (PacBio long reads). PBJelly2 software is used to fill gaps in the assembly using PacBio long reads. The program is designed to handle PacBio data taking its error model into consideration. It uses a PacBio read data‐specific aligner called BLASR (Chaisson and Tesler, 2012) to map PacBio reads to the assembly and attempt to replace Ns with A, C, G or T. The final output from PBJelly2 was the first draft version of the genome.

Tran H.T., Ramaraj T., Furtado A., Lee L.S, & Henry R.J. (2018). Use of a draft genome of coffee (Coffea arabica) to identify SNPs associated with caffeine content. Plant Biotechnology Journal, 16(10), 1756-1766.

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Genome Assembly from Illumina Sequencing

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DNA obtained from clonal cultures (25 °C) of SymA and SymC was used for Illumina library construction (Additional file 1: Table S1), as described previously. Libraries were sequenced using the Illumina Genome Analyzer IIx (GAIIx) and Hiseq (Additional file 1: Table S1). Paired-end reads were assembled de novo with IDBA_UD (ver. 1.1.0) [75 (link)], and subsequent scaffolding was performed with SSPACE (ver. 3.0) [76 (link)] using Illumina mate-pair information. Gaps inside scaffolds were closed with Illumina paired-end data using Gapcloser [77 (link)]. As described previously [4 (link)], sequences that aligned to another sequence by more than 70% using BLASTN (1e^− 100) were removed from the assembly. Scaffolds > 1 kb were added in version 1.0 of the genome assembly.

Shoguchi E., Beedessee G., Tada I., Hisata K., Kawashima T., Takeuchi T., Arakaki N., Fujie M., Koyanagi R., Roy M.C., Kawachi M., Hidaka M., Satoh N, & Shinzato C. (2018). Two divergent Symbiodinium genomes reveal conservation of a gene cluster for sunscreen biosynthesis and recently lost genes. BMC Genomics, 19, 458.

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Hybrid Genome Assembly Workflow

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Quality-checked ONT reads were error-corrected using Illumina PE reads. For error correction, the Illumina PE reads were aligned to the ONT reads using BWA aligner (BWA, RRID:SCR_010910) [16 (link)]. PE reads were assembled using Abyss (ABySS, RRID:SCR_010709) [17 (link)], followed by contig extension using ONT reads using SSPACE-LongRead [18 (link)]. Super-scaffolding of the assembled scaffold was performed using SSPACE (SSPACE, RRID:SCR_005056) [19 (link)] and PLATANUS on the ONT and mate-pair data. A final draft genome resulted after gap closure using GAPCLOSER (GAPCLOSER, RRID:SCR_015026) [20 (link)] and the PLATANUS gap_close tool, with Illumina data. The genome size was estimated with a k-mer distribution plot using JELLYFISH (Jellyfish, RRID:SCR_005491) [21 (link)]. The assembly and annotation workflow is shown in Fig. 2.

Dhar R., Seethy A., Pethusamy K., Singh S., Rohil V., Purkayastha K., Mukherjee I., Goswami S., Singh R., Raj A., Srivastava T., Acharya S., Rajashekhar B, & Karmakar S. (2019). De novo assembly of the Indian blue peacock (Pavo cristatus) genome using Oxford Nanopore technology and Illumina sequencing. GigaScience, 8(5), giz038.

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Hybrid genome assembly using long and linked reads

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PacBio long reads and 10× Genomics linked reads were assembled respectively using CANU [25] (link) and Supernova [26] (link) with default options. Mismatches and small indels in PacBio contigs were corrected using Illumina paired-end reads.
To combine the two data sets of assembled genomes, the PacBio contigs over 50 kb were aligned to the scaffolds assembled from 10× Genomics linked reads using MUMMER [67] , and sequence overlaps between the two data sets were identified and classified to 8 types (Figure S15). Using in-house Perl/Python scripts, 10× Genomics scaffold sequences were substituted with PacBio contigs in the matched regions where PacBio contigs are fully included, and were linked by the PacBio contigs which were mapped to the ends of two 10× Genomics scaffolds. The PacBio contigs with ambiguous alignment to 10× Genomics scaffolds were excluded in the PacBio-10× merging process to avoid the errors on determining sequence overlaps. Then Bionano optical mapping data was used for hybrid scaffolding using Bionano Solve (V3.0.1) [68] (link). Finally, the gaps in hybrid scaffolds were filled with Illumina paired-end reads using Gapcloser [69] (link).

Du Z., Ma L., Qu H., Chen W., Zhang B., Lu X., Zhai W., Sheng X., Sun Y., Li W., Lei M., Qi Q., Yuan N., Shi S., Zeng J., Wang J., Yang Y., Liu Q., Hong Y., Dong L., Zhang Z., Zou D., Wang Y., Song S., Liu F., Fang X., Chen H., Liu X., Xiao J, & Zeng C. (2019). Whole Genome Analyses of Chinese Population and De Novo Assembly of A Northern Han Genome. Genomics, Proteomics & Bioinformatics, 17(3), 229-247.

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