SSPACE-LongRead

[…] the value of hi-c-based scaffolding relative to scaffolding with only pacbio long reads, we assembled the pacbio reads together with the allpaths-based sra1 scaffolds using the hybrid assembler sspace-longread [] and pbjelly2 to produce the aps1 assembly (fig. , table ). relative to the hi-c improved pga2, the aps1 assembly was similar in total length (spanning 400.9 mb) and number […]

[…] bp were filtered out and the remaining contigs were used for downstream analyses., the g. sempervirens assembled contigs were scaffolded using the synthetic long reads longer than 1499 bp and the sspace-longread tool (v1-1) []; the default alignment options and scaffolding options were used. genome assembly quality was evaluated using cegma [] and representation of rna-sequencing reads (see […]

[…] with successive refinement (blasr) (). based on these alignments, the contigs were linked and placed into scaffolds. the orientation, order, and distance between the contigs were estimated using sspace-longread version 1.0 (). using illumina reads, gapped regions within scaffolds were (partially) closed using gapfiller version 1.10 (). finally, assembly errors and nucleotide disagreements […]

[…] reads were mapped to the draft assembly using blasr (). subsequently, the contigs were linked and placed into scaffolds. the orientation, order, and distance between the contigs were estimated using sspace-longread version 1.0 (). using illumina reads, gapped regions within scaffolds were (partially) closed using gapfiller version 1.10 (). finally, assembly errors and nucleotide disagreements […]

[…] with sspace version 3.0 () using the 60,686,211 paired-end reads of 100 bp, leading to an intermediate version of the assemblage containing 9 scaffolds. a final scaffolding step was performed with sspace longread version 1.1 () using the 317,258 pacbio rs-filtered subreads. we finally obtained 3 scaffolds with a total size of 2,084,275 bp (without an unspecified base) and an average coverage […]

[…] high degree of similarity between the sequences of the two genomes.table 1note: 1. step 1: obtained by allpaths-lg assembly.2. step 2: obtained by comparative analysis of allpaths-lg assembly and sspace-longread assembly.3. step 3: obtained by performing jelly implemented in pbsuite based on canu assembly.4. step 4: obtained by performing jelly based on the smrt sequencing data […]

[…] were joined by the minimus2 assembler, which uses an algorithm that calculates overlaps between contigs. on the other hand, the two contigs forming the chromosome 33 could be joined by means of the sspace-longread tool, which selects and uses only the longest pacbio reads to construct a scaffolding. finally, the gap size between pairs of contig was calculated (lower than 5-kb in all cases) […]