Can you assemble with merged paired end reads and unmatched reads as "single ended" reads?
BBMap to isolate
r2 reads while providng unmatched reads as well. It generated a single file. It is wise to use this in my assembler (
SPAdes) as single-ended?
I ended up using the
outm=./bbmap_output/mapped.fq from below as input into
single ended with the
-s flag. My
mapped.fq file has not only paired
r2 reads but also the
bbwrap.sh -Xmx40g in=./reads/r1.fq,$SINGLETONS in2=./reads/r2.fq,null outm=./bbmap_output/mapped.fq outu=./bbmap_output/unmapped.fq ref=./reference/assembly.fa out=./bbmap_output/output.sam lengthtag=t idtag=t covstats=./bbmap_output/output.covstats.txt rpkm=./bbmap_output/output.rpkm.txt threads=$N_JOBS usemodulo append
For SPAdes, my command was the following:
python spades-3.9.0/bin/spades.py -t $N_JOBS -s ./bbmap_output/mapped.fq -o ./spades_output/