PRICE de novo assembly
Robert Edgar edited this page May 19, 2020
·
4 revisions
Here is how I ran price for Frank. I selected SAM records with CIGAR=151M and converted to fastq. The command-line options were suggested by the price author (Graham Ruby). This was my first quick-and-dirty attempt, no optimization attempted. Graham recommend read QC first using the method implemented in the price package but I didn't try that. The command line is messed up below, should have backslashes to continue the line but got lost in the wiki.
fq1=../fq/ERR2756788_1.fastq fq2=../fq/ERR2756788_2.fastq
virus=../fa/ERR2756788_151M.fa
mkdir -p ../price
/usr/bin/time -v -o price.time
$PriceTI -fpp $fq1 $fq2
600 90
-icf $virus
1 1 1
-nc 10
-dbmax 151
-mol 30
-tol 20
-mpi 80
-target 90 0
-trimB 0 1.5
-a 8
-o ../price/contigs.fa
- Accessing Serratus Data
- Data Types
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- PRICE de novo assembly
- Taxonomy case study of misannotated Genbank entry
- Taxonomy prediction
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- Design of nucleotide summarizer scoring and-depth estimates
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