Entering edit mode
5.5 years ago
macielrodriguez2
▴
50
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 :)
How did you install Abyss?
I installed it in an Anaconda environment, with this conda installers: https://anaconda.org/bioconda/abyss