Assemble Drosophila melanogaster with ABySS

I assembled an Illumina short-read sequencing data set of Drosophila melanogaster with ABySS 2.0.1. The data set includes a 2x101 paired-end library and a 2x110 mate-pair library. I assembled the reads with and without adapter trimming the mate-pair library using NxTrim (doi:10.1101/007666), and compared the results of these two methods. I optimized k and N and selected the best assembly (see Methods). I aligned the assembled scaftigs to the reference (BDGP6) using BWA-MEM and calculated assembly metrics using abyss-samtobreak and abyss-fac. I find that the assembly of mate-pair reads trimmed with NxTrim yields an assembly that is both more contiguous (scaffold NGA50) and more correct (fewer breakpoints compared to the reference).

Data

• Paired-end: https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3663859
• Mate-pair: https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3663860

Results

• Report of assembly metrics using RMarkdown
• Assembly metrics of abyss-samtobreak: dmelanogaster.samtobreak.tsv
• Assembly metrics of abyss-abyss-fac: dmelanogaster.abyss-fac.tsv

Methods

I optimized k by trying every value between 32 and 64 with a step size of 8 and selected the assembly with the best NGA50. I optimized N by trying every value between 10 and 25 and selecting the assembly with the best N50.

cd nxtrim/abyss/k48
for n in 5 {10..25}; do
	echo n=$n
	abyss-scaffold -k48 -G143725995 -s1000-10000 -n$n dmelanogaster-6.dot mp1-6.dist.dot 2>&1 >/dev/null | tail -n1
done

Pipeline