MinION sequencing of seafood in Singapore reveals creatively labelled
flatfishes, confused roe, pig DNA in squid balls, and phantom crustaceans

猪肉检测

直接Blast nr ngs reads

Table 2. Comparison of the proposed method in the current study with the previously reported methods of pork detection in foodstuff.

文章中对几个方法也做了对比

丰度偏差

Analysis pipeline for NGS data

1. Quality assessment of DNA reads using FastQC tool
perl fastqc –f fastq File.fastq.gz -o out_directory/

2. Trimming of reads using Trimmomatic tool
java -jar trimmomatic.jar SE File.fastq.gz File.filterd. fastq.gz CROP:90 MINLEN:50

3. Converting the fastq into fasta format
sed -n '1~4s/^@/>/p;2~4p' File.fastq > Outfile.fa
or if the fastq file is in compressed format:
zless File.fastq | sed -n '1~4s/^@/>/p;2~4p' > Outfile.fa

4. BLAST analysis for species matching
blastn -query Input.sequences.fa -db nt -out output-blast-file -remote -subject_besthit -max_target_seqs 5 -outfmt "6 qacc qlen sseqid sacc pident nident mismatch evalue qcovhsp stitle salltitles ssciname scomname" -perc_identity 99

nanopore 非PCR 测序

Flesh ID: Nanopore Sequencing Combined with Offline BLAST Search for the Identification of Meat Source

食物性病原 食物安全