Hi,
I have paired DNA-seq data of some protista. I tried to do assembly using the abyss 2.1.1 after trimming using Trimmomatic. Trimmomatic preprocessed reads into Paired end reads (Forward and Reverse) and unpaired reads from each file that I have considered as single end reads for abyss assembly.
Used command for the abyss
for k in {150..250..10}; do mkdir k$k; cd k$k; abyss-pe k=$k name=1604 pe='../protista_forward_paired.fastq ../protista_reverse_paired.fastq' se='../protista_forward_unpaired.fastq ../protista_reverse_unpaired.fastq'; cd ..; done
I got three contig files like protista_contig-1.fa, protista_contig-2.fa, protista_contig-3.fa.
complete list of output :
coverage.hist, protista-bubbles.fa, protista-1.fa, protista-1.dot, protista-1.path, protista-2.dot1, protista-2.fa, protista-2.dot, protista-3.dot, protista-2.path, protista-3.fa, protista-indel.fa, protista-unitigs.fa , protista-3.fa
I am not sure which config file I should use for further analysis including scaffolding. Could someone please help me with this.
Thank you very much in advance.
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