updated bowtie2 alignment settings for scaffolding via pairs and split segments
updated bowtie2 alignment settings for scaffolding via pairs and split segments

trinityrnaseq/trinityrnaseq,trinityrnaseq/trinityrnaseq,trinityrnaseq/trinityrnaseq,trinityrnaseq/trinityrnaseq,trinityrnaseq/trinityrnaseq,trinityrnaseq/trinityrnaseq,trinityrnaseq/trinityrnaseq