Using library specific value for -l

[Matthew MacManes]

Hi Tony, 

I remember once knowing this, but I cannot remember or find on the google group. 

I am assembling using 300nt PE Miseq reads, and 150NT MP reads using k=127. During MP scaffolding, I need to be able to set -l (----min-align) to something other than 127- using this value hardly anything aligns. I remember there being a way to set -l in a library specific manner, but I can't how..

Command I am using is:

abyss-pe np=8 k=127 name=ecoli lib='pe1' mp='mp1' long='minion' \

pe1='/mnt/ecoli_pe.1.fq /mnt/ecoli_pe.2.fq' \

mp1='/mnt/nextera.1.fq /mnt/nextera.2.fq' \

minion='minion.data.fasta' --dry-run

Thanks, Matt 

[Ben Vandervalk]

Hi Matt,

I'm pretty sure this will work:

$ abyss-pe mp1_l=30 <your other abyss-pe params...>

where "30" is your chosen minimum alignment for the library "mp1".

- Ben

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