2020-11-16 宏基因组中细菌16s rRNA组装分析

export PHYLOFLASH_DBHOME=/nfs_genome/BioDB/138.1/

conda activate phyloflash

for id in `ls /nfs_genome/home/zhaoshanzhong/zs/data/metagenome64/metacleandata/*.filtered.fq1.gz`

do 

id=${id/*\//}

id=${id/.filtered.fq1.gz/}

phyloFlash.pl -lib $id -everything -read1 /nfs_genome/home/zhaoshanzhong/zs/data/metagenome64/metacleandata/$id.filtered.fq1.gz -read2 /nfs_genome/home/zhaoshanzhong/zs/data/metagenome64/metacleandata/$id.filtered.fq2.gz

done