hello, I want to run a co-assembly using multiple samples, I can group together the R1 and R2 reads as shown for three libraries (six read files): megahit [options] {-1 pe1_R1.fq,pe2_R1.fq,pe3_R1.fq -2 pe1_R2.fq,pe2_R2.fq,pe3_R2.fq} -o outdir,
besides, I can also do the following command like: cat _R1.fq > ALL_READS_R1.fq; cat _R2.fq > ALL_READS_R2.fq, and then using megahit to assemble like this: megahit -1 ALL_READS_R1.fq -2 ALL_READS_R2.fq -o outdir.
I want to know the difference of the above two methods, Is the result of one better than the other？
Looking forward to your reply，thanks
hello, I want to run a co-assembly using multiple samples, I can group together the R1 and R2 reads as shown for three libraries (six read files): megahit [options] {-1 pe1_R1.fq,pe2_R1.fq,pe3_R1.fq -2 pe1_R2.fq,pe2_R2.fq,pe3_R2.fq} -o outdir, besides, I can also do the following command like: cat _R1.fq > ALL_READS_R1.fq; cat _R2.fq > ALL_READS_R2.fq, and then using megahit to assemble like this: megahit -1 ALL_READS_R1.fq -2 ALL_READS_R2.fq -o outdir. I want to know the difference of the above two methods, Is the result of one better than the other？ Looking forward to your reply，thanks