SRR4240358

mkdir pr15

wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR424/008/SRR4240358/SRR4240358.fastq.gz

cp /mnt/scratch/NGS/adapters/* /mnt/scratch/NGS/lidia/pr15

cat *.fa > adapters.fasta

java -jar /usr/share/java/trimmomatic.jar SE -phred33 -threads 12 SRR4240358.fastq.gz clear_reads.fastq.gz ILLUMINACLIP:adapters.fasta:2:7:7 2> log_trimmomatic.txt

java -jar /usr/share/java/trimmomatic.jar SE -phred33 -threads 12 clear_reads.fastq.gz new_clear_reads.fastq.gz TRAILING:20 MINLEN:32 2> log_trimmomatic2.txt

velveth velveth 31 -fastq -short new_clear_reads.fastq.gz

velvetg velveth 1> log_velveg

sort -n -r -k 2 stats.txt | more

seqret contigs.fa:NODE_56_length_19821_cov_29.475859

seqret contigs.fa:NODE_34_length_18714_cov_29.922678

seqret contigs.fa:NODE_40_length_16436_cov_30.793623