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Old 07-07-2016, 08:20 AM   #1
yvan.wenger
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Location: Switzerland

Join Date: Aug 2009
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Default MaSuRCA adapter trimming

Hello,

I am currently trying MaSuRCA, I get nice results but I think they can be further improved.

I made some test on a subset of reads, with or without clipping adapters before passing it to MaSuRCA. As advised in the short manual, I got better results with the full reads.

When quorum starts it says in quorum.err: "Loading contaminant sequences", so I assume that there is somewhere a contaminant library, such as for example masurca/share/adapters.jf

in the output PREFIX.cor.fa, I have plenty of my adapters, how can I specify my adapter sequences to quorum/MaSuRCA? Should I make a new adapters.jf file? My adapters are simple illumina TruSeq.

Has somebody done that?

Many thanks for all your thoughts !

Yvan
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Old 07-07-2016, 08:45 AM   #2
yvan.wenger
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Default

Ooops, I*should have had a more careful look. While I*don't know what is exactly in the share/adapter.jf I*made my own:

../bin/jellyfish count -m 24 -s 5k -C -t 10 -o adapters_yvan.jf adapters.fa && mv adapter.jf adapter.jf_old && ln -s adapters_yvan.jf adapter.jf

And it works well. I could have deleted the post but some might find it useful.

Best,

Yvan
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