Computational protocol: Reassociation kinetics-based approach for partial genome sequencing of the cattle tick, Rhipicephalus (Boophilus) microplus

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Protocol publication

[…] The fasta and quality files were extracted from the 454 reads (unpaired) in the Standard Flowgram Format (SFF) files using the python script 'sff_extract.py' and the random first 9-mer and 4 tcag clipped. Mira V2.9.43 [] was used to assemble the 454 reads against an existing sequence backbone of the BmiGI Version 2.1 gene index [,]. Mira options were selected for an accurate highly repetitive 454 assembly. The 454 reads were mapped to the assembled BAC sequences using Maq Version: 0.7.0 alignment tool (http://maq.sourceforge.net/maq-man.shtml#intro) and the Newbler assembler Software Release: 2.0.00.20 []. The alignments were visualized using BioPerl scripts []. For our BAC study, BLAST hits having e-values below 0.001 were considered as significant hits. NUCmer version 3.06 at default settings [] was used to visualize the repetitive nature of the BACs. Genscan was utilized to identify open reading frame matches to GenBank entries []. […]

Pipeline specifications

Software tools seq_crumbs, Newbler, BioPerl, MUMmer, GENSCAN
Applications WGS analysis, Nucleotide sequence alignment
Organisms Rhipicephalus microplus