doc/pauda_changes.md

In jkruppa/viralDetectTools: Modules for a viral detection pipeline

Changes to the Pauda source code

Source

Original source: http://ab.inf.uni-tuebingen.de/data/software/pauda/download/welcome.html

Changes

Several changes to the Pauda implementation were necessary to fulfill our requirements. The following Table shows all changes with the connected program line. First, we changed the command -Xmx, which specified the maximum memory allocation pool to 50 GB in all shell scripts. This was needed to allow Pauda to handle the large amino acid reference genome. Second, we changed some Bowtie2 parameters. We set -N, the number of mismatches to be allowed in a seed alignment from 1 back to the default value of 0. This makes the alignment less sensitive but much faster. We set -K from 30 to 100, allowing Bowtie2 up to one hundred multi maps per read. Finally, we set -score-min from 35 to 10, which is the minimum score for a alignment to be judged as valid.

| Source file | Line | From | To | |------------- |-------------| -----|-----| | z1_protein2pna.sh | 56 | --Xmx20 | --Xmx50| | z4_bowtie-on-pna.sh | 26 | bowtie2-align | bowtie2| | | 45 | N=1 | N=0| | | 46 | K=30 | K=100| | | 49 | MS=35 | MS=10| | z5_sam2blastx.sh | 50 | --Xmx8 | --Xmx50| | | 59 | --Xmx8 | --Xmx50| | z6_blastx2rma.sh | 27 | --Xmx8 | --Xmx50|

jkruppa/viralDetectTools documentation built on May 30, 2019, 3:41 p.m.