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1.md5sum+trimmomatic

md5sum SRR1976948_1.fastq.gz SRR1976948_2.fastq.gz

java -jar /data/XXXXX/software/software/Trimmomatic-0.36/trimmomatic-0.36.jar PE \
-phred33 SRR1976948_1.fastq.gz SRR1976948_2.fastq.gz \
/data/XXXXX/test/MGS/01trim/SRR1976948_1_paired.fq.gz \
/data/XXXXX/test/MGS/01trim/SRR1976948_1_unpaired.fq.gz \
/data/XXXXX/test/MGS/01trim/SRR1976948_2_paired.fq.gz \
/data/XXXXX/test/MGS/01trim/SRR1976948_2_unpaired.fq.gz \
ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

Remove adapters (ILLUMINACLIP:TruSeq3-PE.fa:2:30:10)
Remove leading low quality or N bases (below quality 3) (LEADING:3)
Remove trailing low quality or N bases (below quality 3) (TRAILING:3)
Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 15 (SLIDINGWINDOW:4:15)
Drop reads below the 36 bases long (MINLEN:36)

2.fastqc

fastqc SRR1976948_1_paired.fq.gz
fastqc SRR1976948_2_paired.fq.gz

3.MEGAHIT

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