Table 9.
List of open source tools used in our study of the alternatives to the LifeScope pipeline
| Analysis category | Tool | Web reference |
|---|---|---|
| Convert XSQ to color-space fastq | XSQtools solid2fastq | Life Technologies website Bfast package |
| Alignment to the reference genome | Maq v.0.7.1 | http://maq.sourceforge.net/ |
| Default parameters, -n 3 | ||
| Shrimp 2.2.3 | http://compbio.cs.toronto.edu/shrimp/ | |
| Default parameters, -h 85 –strata -o 3 | ||
| Bfast 0.7.0 | http://sourceforge.net/projects/bfast/ | |
| Default parameters | ||
| Preprocessing | Picard 1.111 | http://picard.sourceforge.net/ |
| Samtools 0.1.18 | http://samtools.sourceforge.net/ | |
| Variant calling | GATK v.3.1 | http://www.broadinstitute.org/gatk/ |
| Steps and parameters in Table 7 | ||
| Variant summaries | Vcftools 0.1.12 | http://vcftools.sourceforge.net/ |
| Bcftools v.0.2.0 | http://samtools.github.io/bcftools/ | |
| Variant annotation | Annovar | http://www.openbioinformatics.org/annovar/ |