How To Tune Parameters When Running Shrimp2 On Longer Illumina Reads

Question

[kanwarjag]

I have been working with Miseq data (150bp) PE reads for detection of sequence variation in bacterial genome (~10Kb). I found only SHRIMP2 is giving me best possible alignments, which I can see in a genome browser. However, I just used the default options:

gmapper-ls -N 12 -s 11110111101111,1111011100100001111,1111000011001101111 -o 10 --max-alignments 0 -w 140.0% -n 2 --qv-offset 33 -m 10 -i -15 -g -33 -q -33 -e -7 -f -3 -r 0.0 -h 0.0 -I 0,1000 --longest-read 1000 -H –un

I have not found much of the literature which suggest that SHRIMP is used for Illiumina reads (It has been mainly used for color space reads) . I read one paper: A novel and well-defined benchmarking method for second generation read mapping which suggest that for longer reads –“weighted seeds to be used to improve performance for longer reads” While reading manual of SHRIMP I could not find this specific feature. So here is what I need expert helps from this forum’s users:

1. Can I use SHRIMP2 for Illumina long reads (150bp) and small insert, My aim is to look for seq variation.
2. There are several parameters which can be fine tuned, there is no best practice parameters mentioned for SHRIPM, If some one has used this aligner for longer illumine read can share best possible parameters or pointer for best parameters .
3. Where should I find ‘weighted seeds’ option in SHRIMP.

Thanks

Kanwar

[Istvan Albert]

I sent an email to the shrimp newsgroup via the request help feature above. Hopefully they will provide some answers.