Minia

[…] Genomics Workbench, and CodonCode Aligner); the others are freely available for academic purposes. Since de Bruijn graphs are inescapable (they are used by A5-miseq, CLC Genomics Workbench, Geneious, Minia, MIRA, SOAPdenovo2, SPAdes, and Velvet), we made an effort to also include different assembly methods, including Overlap-Layout-Consensus (CodonCode Aligner), string graph (fermi), and greedy al […]

[…] 5 paired‐end library, indicating that the peak frequency of K depth was about 21. Error correcting was undertaken using Allpaths‐lg's tools (Gnerre et al., ). De novo contig assembly was conducted by Minia v1.6906 (Chikhi and Rizk, ). SSPACE‐STANDARD‐3.0 (Boetzer et al., ) was used to link contigs into scaffolds with mate‐pair reads. Gaps in scaffolds_1 were filled using PBJelly 14.9.9 (English et […]

[…] eatMasker v1.317 [], SNAP [], and Augustus v3.0.1 []. SNAP utilized a scabies mite Hidden Markov Model (HMM) generated previously [] and Augustus used the BUSCO-generated model from the k = 47, m = 7 Minia assembly. Hints for gene predictions were based on 17,091 EST sequences from other Sarcoptiformes mites (NCBI EST database), and the CEGMA 458 core proteins []. Over 200 of the Maker predictions […]

[…] gaps characterized by Ns in the Ragout assembly. Also worth noting with the Marseille strain, MeDuSa was not able to correct a larger than expected contig assembly obtained with SPAdes. Finally, the Minia-AGapEs assemblies did not contain Ns due to the filling of the gaps uncovered by reads by the template sequence, we have indicated the length of template sequence used in parentheses instead. […]

[…] T, all the algorithms presented are based on an efficient representation of the de Bruijn graph with optimized bloom filters, implemented in the GATB C++ library [], as used for the first time in the MINIA [, ] assembler.A bloom filter is a probabilistic data structure that stores the presence/absence of items. It consists of a simple bit vector, initially all set to ‘0’. Any item is associated wi […]

[…] atic v. 0.35 (), with a minimum leading and trailing sequence quality of 5, and a minimum internal sequence quality of 5 using a sliding window of 4 bp. An initial de novo assembly was performed with Minia 1.6906 (; ), with a k-mer size of 53 and a minimum k-mer depth of 4.Inspection of the resulting contigs revealed the presence of sequences from two distinct Rickettsiella-like endosymbionts. One […]