Assembly¶

Use IDBA_UD to make a co-assembly of your reads

Source the configuration file:

source conf_cluster.conf

First, create a directory for saving assembly files and concatenate R1 and R2 reads into two files:

mkdir -p $ASSEMB_READS
cat $FILT_READS/filtered*R1*fastq > $ASSEMB_READS/cat.filtered.$PRJ_NAME.R1.fastq
cat $FILT_READS/filtered*R2*fastq > $ASSEMB_READS/cat.filtered.$PRJ_NAME.R2.fastq

Now, prepare the input files for IDBA_UD that requires interleaved FastA format:

fq2fa --merge $ASSEMB_READS/cat.filtered.$PRJ_NAME.R1.fastq $ASSEMB_READS/cat.filtered.$PRJ_NAME.R2.fastq $ASSEMB_READS/interleaved.cat.filtered.$PRJ_NAME.fasta

See assembly parameters:

echo "MIN_KMER_LEN= " $MIN_KMER_LEN
echo "MAX_KMER_LEN= " $MAX_KMER_LEN
echo "STEP= " $STEP

Run IDBA_UD:

idba_ud -l $ASSEMB_READS/interleaved.cat.filtered.$PRJ_NAME.fasta \
-o $ASSEMB_READS/d.$PRJ_NAME.idba \
--mink $MIN_KMER_LEN \
--maxk $MAX_KMER_LEN \
--step $STEP \
--pre_correction \
--num_threads 12

Have a look to the obtained files:

cd $ASSEMB_READS/d.$PRJ_NAME.idba
ll