#!/bin/bash

This script is used to assemble paired-end reads after fragmentation.

Set the input and output file names

input1="read1.fastq" input2="read2.fastq" output="assembled.fasta"

Set the parameters for the assembler

kmer=31 min_overlap=100 max_overlap=500 n_threads=4

Fragment the reads

echo "Fragmenting reads..." frag1=$(echo $input1 | sed 's/.fastq/.frag1.fastq/') frag2=$(echo $input2 | sed 's/.fastq/.frag2.fastq/') fragfasta=$(echo $output | sed 's/.fasta/.frags.fasta/') flash $input1 $input2 -o frags -t $min_overlap -p $max_overlap -m $kmer -x 0.3 -d ./ -z -o $n_threads

Assemble the fragments

echo "Assembling fragments..." spades.py -1 $frag1 -2 $frag2 --careful -t $n_threads -o spades_out

Merge the contigs

echo "Merging contigs..." contigs=$(echo $output | sed 's/.fasta/.contigs.fasta/') cat spades_out/contigs.fasta | tr ' ' '_' > $contigs

Clean up

echo "Cleaning up..." rm -f $frag1 $frag2 $fragfasta rm -rf frags rm -rf spades_out

echo "Done!"