Mercurial > repos > trungnguyencoffee97ktest > nanopore_sanger
comparison nanoclust.sh @ 0:cc560d7f391a draft default tip
Uploaded a bash file to test
| author | trungnguyencoffee97ktest |
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| date | Wed, 01 Jun 2022 07:02:10 +0000 |
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| -1:000000000000 | 0:cc560d7f391a |
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| 1 #! /bin/bash | |
| 2 ## This code is invented to test NanoporeSanger pipeline, in which we use barrnap to extract 16S ribosomal of bacteria, and use it for taxonomy | |
| 3 set -ux | |
| 4 export THREADS=20 | |
| 5 export nextflow='/media/kt/data/0.Tools/nextflow/nextflow' | |
| 6 export nanoclust_main='/media/kt/data/TRUNG/2.Tool/NanoCLUST/main.nf' | |
| 7 export seqtk='/media/kt/data/anaconda3/envs/kt/bin/seqtk' | |
| 8 export outdir='/media/kt/data/TRUNG/0.Projects/13.NANOPORE-SANGER/3.Output/NanoClust/16SNCBI_REFFSEQ' | |
| 9 export db16Sncbi='/media/kt/data/TRUNG/2.Tool/NanoCLUST/db/16S_ribosomal_RNA' | |
| 10 export db16Ssilva_nr_ref='/media/kt/data/TRUNG/3.Database/database_sliva/Nonredundant_Ref/SILVA_138-1_nr_ref' | |
| 11 export taxdbncbi="/media/kt/data/TRUNG/2.Tool/NanoCLUST/db/taxdb/" | |
| 12 | |
| 13 | |
| 14 longread='/media/kt/data/TRUNG/0.Projects/13.NANOPORE-SANGER/3.Output/Nanopore_reads_of_GCF_000196035.1_ASM19603v1_genomic.trimmed.fastq.gz' | |
| 15 allreads='' | |
| 16 for nread in {100,500,1000,1500,2000}; do | |
| 17 prefix=$(basename -s .fastq.gz $longread) | |
| 18 #capacity=$(awk "BEGIN {print int($nread*1500/10**6+0.5)}") | |
| 19 mkdir -p $outdir/${prefix} | |
| 20 outread=$outdir/${prefix}/${prefix}_${nread}_reads.fastq.gz | |
| 21 $seqtk sample -s50 $longread $nread | gzip > $outread | |
| 22 $nextflow $nanoclust_main -profile docker --reads $outread --outdir $outdir/$prefix/${prefix}_${nread}_reads \ | |
| 23 --db $db16Sncbi --tax $taxdbncbi | |
| 24 done |