Sentence examples for 1 abyss from inspiring English sources

In the assembly of the UCRNP2 dataset (see Table-S2; Additional file 1), ABySS and IDBA-UD show higher g1 quality performance as compared to the current draft genome at both contigs and scaffolds levels (see Fig. S2; Additional file 2).

In the assembly of UCREL1 dataset (see Table-S4; Additional file 1), ABySS, IDBA-UD, and SPAdes exhibit high quality g1 metrics performance, which is better than the performance of the current draft genome (df_1) at the contigs level, while ABySS, IDBA-UD, SPAdes and Velvet have better g1 metrics performance than df_1 at the scaffolds level (see Fig. S4; Additional file 2).

dkmer size was iteratively set to 21, 25, 31, 41, 51 for ABySS, SOAPdenovo and velvet.

Some examples of these tools are Velvet [ 1], ABySS [ 2], Euler [ 3], SOAPdenovo [ 4] and ALLPATHS [ 5].

Some of the assemblers using this Eulerian-based approach include EULER [ 21], VELVET [ 22], ABYSS [ 6] and ALLPATHS [ 23].

de novo human genome (NA18507) assemblies reported by our assembler (Minia), Conway and Bromage assembler [ 9], ABySS [ 8], and SOAPdenovo [ 7].

For each strain and assembler, n = 27 (SOAPdenovo) or n = 10 (AbySS) separate assemblies were produced, in each case iterating K from 31 to 81.

This suggested that when using the same k-mer size of 25, ABySS and Trinity still had a large proportion of unique bases.

Assembly of Illumina-only data was conducted using the SPAdes [ 34], Velvet [ 35], Abyss [ 36] and the CLC Genomics Workbench (CLC Bio) assemblers and the best results were obtained by the Velvet assembler (Table  2).

(3) ABySS v. 1.3.4 [ 6] was used with k-mer sizes 21, 31, 41, 51 and 61, and contigs were filtered, extended and merged using Trans-ABySS v. 1.4.4 [ 5]. (4) SOAPdenovo-Trans v. 1.01 [ 7] was used with k-mer sizes 21, 31, 41, 51, 61 and 71 with default settings.

Different methods, either based on a de Bruijn graph [Velvet (Zerbino and Birney, 2008), ABySS (Simpson et al., 2009) and SPAdes (Bankevich et al., 2012)] or on a greedy approach [SSAKE, Edena (Hernandez et al., 2008)], are available in Orione.