gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output

Abstract

Unknown sequences, or gaps, are present in many published genomes across public databases. Gap filling is an important finishing step in de novo genome assembly, especially in large genomes. The gap filling problem is nontrivial and while there are many computational tools partially solving the problem, several have shortcomings as to the reliability and correctness of the output, i.e. the gap filled draft genome. SSPACE-LongRead is a scaffolding tool that utilizes long reads from multiple third-generation sequencing platforms in finding links between contigs and combining them. The long reads potentially contain sequence information to fill the gaps created in the scaffolding, but SSPACE-LongRead currently lacks this functionality. We present an automated pipeline called gapFinisher to process SSPACE-LongRead output to fill gaps after the scaffolding. gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines. We compare the performance of gapFinisher against two other published gap filling tools PBJelly and GMcloser. We conclude that gapFinisher can fill gaps in draft genomes quickly and reliably. In addition, the serial design of gapFinisher makes it scale well from prokaryote genomes to larger genomes with no increase in the computational footprint.

The genome and lifestage-specific transcriptomes of a plant-parasitic nematode and its host reveal susceptibility genes involved in trans-kingdom synthesis of vitamin B5

“…Haplotigs and either extremely high or extremely low coverage contigs were removed (using purge haplotigs (a-70)) (Roach, Schmidt, and Borneman 2018). Remaining contigs were upgraded using FinisherSC (Lam et al 2015) and scaffolded using iterative rounds of SSPACE_longreads (Boetzer and Pirovano 2014) and gapFinisher (Kammonen et al 2019): Round 1 (error corrected reads, -k 1 -o 1000 -l 10 -g 500); round 2 (error corrected reads,-k 1 -o 1000 -l 5); and finally round 3 (raw reads, -k 1 -o 1000 -l 30). Scaffolds were then polished with three rounds of arrow (raw PacBio reads, smrttools-release_6.0.0.47835, in --diploid mode), and five rounds of Pilon (raw PacBio reads mapped with minimap2, 150 bp Illumina read pairs mapped with BWA-mem).…”

Comparative Genomics Reveals Insights into the Divergent Evolution of Astigmatic Mites and Household Pest Adaptations

“…For S. scabiei, all Illumina short reads were assembled with SPAdes v3.13.1 85 into the first draft genome. Then, scaffolding was performed by SSPACE Basic v2.0 75 with paired-end Illumina short reads, followed by gap filling using GapFiller v1.10 86 and GapFinisher v1.1 87 . Finally, sequence polishing was completed by Pilon v1.22 79 with all reads and the final genome assembly was generated.…”

Chromosome-levelde novogenome assembly ofTelopea speciosissima(New South Wales waratah) using long-reads, linked-reads and Hi-C

“…Then, the 10x reads were incorporated by short-read polishing using Pilon (Pilon, RRID:SCR_014731) v1.23 [51] with reads mapped using Minimap2 v2.12 [41] and correcting for indels only; we found correcting for indels only resulted in a higher BUSCO score than correcting for indels and SNPs following the steps described in this section. We scaffolded using SSPACE-LongRead v1.1 [52] followed by gap-filling using gapFinisher v20190917 [53]. The assembly was scaffolded from 209 contigs into 138 scaffolds, however, no gaps were filled.…”