Part 3: Single cell genome assembly

3.x.x Merging reads with SeqPrep

This part is only for the ones that will work on Merged reads. Skip this if you do the assembly on the raw reads
To merge read pairs that have significant overlaps, we will use the tool called ‘SeqPrep’.

First, create a folder where to store the output then merge the reads:

mkdir merged_reads
SeqPrep -q 30 -f G5_${sample}_1.fastq -r G5_${sample}_2.fastq \
-1 merged_reads/G5_${sample}_merge_1.fastq.gz \
-2 merged_reads/G5_${sample}_merge_2.fastq.gz \
-s merged_reads/G5_${sample}_merged.fastq.gz

Note that SeqPrep merges read pairs if overlaps between the read pairs are identified. Quality threshold of 30, for example, can be specified by -q 30 flag for overlaps with some mismatches to be counted. It can also remove adapter sequences optionally.