ABySS

[…] ible sequencing errors based on the distribution of Kmer frequencies using SOAPec v2.01 with default settings []. We then built de novo assemblies from the edited reads using SOAPdenovo2 v2.04 [] and ABySS v1.9.0 []. We also assembled the genome with MaSuRCA v2.3.2 [], which uses its own raw data quality control tools. For computational feasibility, the three assemblies used Kmer values of 63, 63, […]

[…] pair-ends. Raw reads were trimmed with an in house perl script to remove low quality reads (N > 10%, or sQ ≤ 5) and reads with adaptor contamination. Clean reads were then de novo assembled using the AbySS assembler version 1.3.5 [], with a Kmer value of 50. GapFiller version 2.0 [] was used to further fill gaps and generate scaffolds. The generated genome assembly was deposited at GenBank under a […]

[…] jei (mix of several individuals) []. Previously obtained 454 transcriptomic data for Microcosmus squamiger [] were also considered. De novo assemblies were conducted with Trinity [] for 454 reads and ABySS [] for Illumina reads using the programs’ default parameters. For both kinds of libraries, we confirmed the sample taxonomic identifications by assembling the mitochondrial cytochrome c oxidase […]

[…] lity regions were filtered out with Trimmomatic software (), and the final data set contained 2,294,412 high-quality paired-end reads. De novo assembly was performed on the error-corrected reads with AbySS (), Velvet (), and SPAdes () bioinformatics tools; the SPAdes software produced the best assemblies, which were further evaluated with QUAST (). The final assembly contained 207 contigs, with a […]

[…] version 2.05, a GenomeScan in-house pipeline, was used for adapter removal and quality checking; bases with a Phred score above Q22 and reads longer than 36 bp passed the filtering. For the assembly, ABySS version 1.3.7 (), with a k-mer length of 64, was used. Scaffolds shorter than 500 bp were removed. A total of 1,367 contigs were used for the assembly of the 34.66-Mb genome. The GC content was […]

[…] tatistical inference []) support task continuation on an ad hoc basis, but formal intermediate checkpoints are found in only a handful of multistage tools such as the genome assemblers MaSuRCA [] and ABySS [].Second, NGS software tools could provide the ability to limit the amount of RAM used. NGS tools that allow the user to specify memory limits are few in number; Java-based tools and the assemb […]