1. Input files

1. Input files for the pipeline are the output files from Trimmomatic using command:

while read f; do java -jar /usr/local/Cellar/trimmomatic/0.36/share/java/trimmomatic-0.36.jar PE -phred33 "$f"_1.fastq.gz "$f"_2.fastq.gz "$f"_forward_paired.fq.gz "$f"_forward_unpaired.fq.gz "$f"_reverse_paired.fq.gz "$f"_reverse_unpaired.fq.gz ILLUMINACLIP:/usr/local/Cellar/trimmomatic/0.36/share/trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 ; done < acc1234

acc1234 is a list of my accessions.

For downstream analysis I used only forward_paired, reverse_paired and forward_unpaired.

Didn't use the reverse_unpaired, couldn't insert 2 reverse files in the spades command.

Similar situation using the HybPiper pipeline. What is the impact of not using the reverse_unpaired reads? How many reads am I throwing away? Any impact on phylogeny inference?