Hi everyone! I'm new in the process of assembling a genome so, please, forgive my mistakes.
I was trying to find the optimal k parameter with the Abyss assembler. For that I followed the manual and wrote this bash script:
#!/bin/bash for k in `seq 20 8 90`; do mkdir k$k abyss-pe np=4 -C k$k k=$k name=cloroplast lib='pea' \ pea='../../../ZM1/ZM1_R1.fastq ../../../ZM1/ZM1_R2.fastq' done abyss-fac k*/cloroplast-contigs.fa
Can someone tell me what did I do wrong? Thank you in advance :)