A method based on ultra performance liquid chromatography-tandem mass spectrometry ( UPLC-MS/MS) has been proposed for the determination of coccidiostat residues in chicken skin and fat. The sample was extracted with the combination of methanol, acetonitrile, and acetic acid, and cleaned-up by Sep-Pak tC18 solid phase extraction cartridge. Data acquisition under positive electrospray mode was performed by applying multiple reaction monitoring for both identification and quantification. The limits of detection and quantification for halofuginone and robenidine were 7 μg/kg and 20 μg/kg, respectively. The limit of detection of salinomycin, monensin, narasin, maduramicin, and lasalocid was 5 μg/kg, and limit of quantification was 15 μg/kg. The recovery was 75% to 110% in the spiked concentration range from 15 μg/kg to 200 μg/kg, with intra-day precision lower than 12. 8%, and inter-day precision lower than 13 . 4%.

The rapid development of high-throughput sequencing technologies has led to a dramatic decrease in the money and time required for de novo genome sequencing or genome resequencing projects, with new genome sequences constantly released every week. Among such projects, the plethora of updated genome assemblies induces the requirement of version-dependent annotation files and other compatible public dataset for downstream analysis. To handle these tasks in an efficient manner, we developed the reference-based genome assembly and annotation tool (RGAAT), a flexible toolkit for resequencing-based consensus building and annotation update. RGAAT can detect sequence variants with comparable precision, specificity, and sensitivity to GATK and with higher precision and specificity than Freebayes and SAMtools on four DNA-seq datasets tested in this study. RGAAT can also identify sequence variants based on cross-cultivar or cross-version genomic alignments. Unlike GATK and SAMtools/BCFtools, RGAAT builds the consensus sequence by taking into account the true allele frequency. Finally, RGAAT generates a coordinate conversion file between the reference and query genomes using sequence variants and supports annotation file transfer. Compared to the rapid annotation transfer tool (RATT), RGAAT displays better performance characteristics for annotation transfer between different genome assemblies, strains, and species. In addition, RGAAT can be used for genome modification, genome comparison, and coordinate conversion. RGAAT is available at https://sourceforge.net/projects/rgaat/ and https://github.com/wushyer/RGAAT_v2 at no cost.
Genome ; Genomics ; High-Throughput Nucleotide Sequencing ; methods ; standards ; Humans ; Reference Standards ; Sequence Analysis, DNA ; methods ; standards ; Software