I am using Abyss for assembling paired end Illimuna metagenomic data after comparing forward and reverse reads in two different files and left owers in two other seperate files as follows:
abyss-pe -j10 k=41 n=2 name=Assembly_1 lib='lib1' lib1='../Common_forword_1.fq ../Common_reverse_2.fq' se='../Forword_unique_1.fq ../Reverse_unique_2.fq'
I got the assmebled contigs.
Now when I wish to join the common reads in forward and reverse reads and give it to Abyss for assembly to check if there's some imporvement over the one I already gave.
I have combined all common reads in forward and reverse reads in a single file, concatenated with flash not combined reads and unique forward and unique reverse reads and gave abyss to assemble.
abyss-pe -j10 k=41 n=2 name=Assembly_1 se='../K5_Flash_Combined_NC_FU_RU.fastq'
But the problem is that when I give it to Abyss, it starts assembly, compleats it but dosen't give any contige file.
I was wondering why? Any suggestions will be helpful. Am I doing it wrong? I am new to this so please suggest anything I can try. Thanks a lot.