32 lines
1.2 KiB
Bash
32 lines
1.2 KiB
Bash
#! /bin/bash
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set -e
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SCRIPTS=${SCRIPTS:-"$PROJECTHOME/99.scripts"}
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MAX_MEMORY=${MAX_MEMORY:-"20G"}
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VIRIDI=${VIRIDI:-"$PROJECTHOME/01.reference/viridiplantae_odb12/"}
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ROSALES=${ROSALES:-"$PROJECTHOME/01.reference/rosales_odb12/"}
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if [ "$#" -ne 4 ]; then
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echo "Usage: $0 <reads_1.fastq> <reads_2.fastq> <stem> <threads>"
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echo "Perform de novo transcriptome assembly using Trinity"
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exit 1
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fi
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fq1=$1
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fq2=$2
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stem=$3
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outdir="$stem"_trinity_out_dir
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THREADS=$4
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# Run Trinity for de novo transcriptome assembly
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Trinity --seqType fq --left "$fq1" --right "$fq2" --CPU "$THREADS" --max_memory "$MAX_MEMORY" --output "$outdir"
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# Get Longest isoform per gene
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perl "$SCRIPTS"/trinity_utils/util/misc/get_longest_isoform_seq_per_trinity_gene.pl "$outdir.Trinity.fasta" >"$outdir".longest_isoform.fasta
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# BUSCO assessment
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busco -i "$outdir".longest_isoform.fasta -l "$VIRIDI" -m tran --cpu "$THREADS" -o "$outdir"_busco_viridi -f
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busco -i "$outdir".longest_isoform.fasta -l "$ROSALES" -m tran --cpu "$THREADS" -o "$outdir"_busco_rosales -f
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# Length Statistics
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TrinityStats.pl "$outdir.Trinity.fasta" >"$outdir".Trinity.fasta.length_stat.txt
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# Clear temporary directory
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rm -rf "$outdir"
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