I have used Illumina GA II to sequence two pairend DNA libraries,
one were sequenced with forward reverse direction, -500 bp insert size (LIB1 FR)
the other were sequenced with reverse forward direction, -2kb insert size ,this library was built after circulation. (LIB2 RF)
When I assemly the reads, I got curious results. If I did not reverse complement the second library, I got lower N50 values, but with more reads could be assemblied. (N50 25k, 480M scaffolds/contigs were assembled)
When I reverse complement the second librayry, I got higher N50 values, buit with many reads that could not be assemblied. (N50 46k, only 360M scaffolds/contigs were assembled)
I though the second setting (reverse complement LIB2 reads) was right, but how could the wrong setting assembled more contigs/scaffolds?
The assembler i used is SOAPdenovo.