I am trying out novoalign to map paired-end reads from illumina data.
Here is the command line I am using:
Is novoalign really not capable of mapping with FASTA formatted reference? Is there a specific parameter I am missing to use FASTA?
Thanks for any help.
Here is the command line I am using:
Code:
./novoalign -o SAM -d ref.fa -f 1_1.fastq 1_2.fastq
Thanks for any help.
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