Combining de novo and reference-guided assembly with scaffold_builder

Abstract

Genome sequencing has become routine, however genome assembly still remains a challenge despite the computational advances in the last decade. In particular, the abundance of repeat elements in genomes makes it difficult to assemble them into a single complete sequence. Identical repeats shorter than the average read length can generally be assembled without issue. However, longer repeats such as ribosomal RNA operons cannot be accurately assembled using existing tools. The application Scaffold_builder was designed to generate scaffolds – super contigs of sequences joined by N-bases – based on the similarity to a closely related reference sequence. This is independent of mate-pair information and can be used complementarily for genome assembly, e.g. when mate-pairs are not available or have already been exploited. Scaffold_builder was evaluated using simulated pyrosequencing reads of the bacterial genomes Escherichia coli 042, Lactobacillus salivarius UCC118 and Salmonella enterica subsp. enterica serovar Typhi str. P-stx-12. Moreover, we sequenced two genomes from Salmonella enterica serovar Typhimurium LT2 G455 and Salmonella enterica serovar Typhimurium SDT1291 and show that Scaffold_builder decreases the number of contig sequences by 53% while more than doubling their average length. Scaffold_builder is written in Python and is available at http://edwards.sdsu.edu/scaffold_builder. A web-based implementation is additionally provided to allow users to submit a reference genome and a set of contigs to be scaffolded.

First Fatality Associated with Elephant Endotheliotropic Herpesvirus 5 in an Asian Elephant: Pathological Findings and Complete Viral Genome Sequence

“…Unmapped read pairs were extracted by using Samtools v. 0.1.1818, and contigs were assembled de novo by using ABySS19. Scaffold_builder20 was used to produce a draft sequence by ordering the contigs against the EEHV1A/Raman genome sequence. Additional contigs were incorporated, and gaps were closed by using Megamerger21, GapFiller v. 1–1122, and custom Perl scripts.…”

Characterization and Phylogenetic Analysis of Chloroplast and Mitochondria Genomes from the Antarctic Polytrichaceae Species Polytrichum juniperinum and Polytrichum strictum

“…It is possible that these regions were not sequenced and therefore not included in the percentage of genome coverage or these genes probably have a high degree of rearrangement (deletions, tandem duplications, and inversions) and substitutions. Scaffold Builder assembler version 2.2 is not effective when the sequences have a high degree of rearrangements [23], and the sequences of these genes and sequences of the genome have at least 80% identity. These genes were not accounted for during our analysis, and further studies on the presence/absence of these genes in Polytrichaceae mosses are required.…”

“…These genes were not accounted for during our analysis, and further studies on the presence/absence of these genes in Polytrichaceae mosses are required. [23], and the sequences of these genes and sequences of the genome have at least 80% identity. These genes were not accounted for during our analysis, and further studies on the presence/absence of these genes in Polytrichaceae mosses are required.…”

Draft Genome Sequences of Four Alkaliphilic Bacteria Belonging to the Anaerobacillus Genus

“…The resulting assemblies were combined into a consensus assembly for each genome using CISA (contigs less than 1 kb were removed) (16), and this was later aligned to the previously published A. macyae DSM 16346 genome (GenBank accession no. LELK01000000) and scaffolded using Scaffold_Builder version 2.2 (17). Annotation of the genomes was performed using the NCBI Prokaryotic Genome Annotation Pipeline after sequence submission to GenBank.…”