Main tool: SPN_Serotyper.pl
Code repository: https://github.com/BenJamesMetcalf/Spn_Scripts_Reference
Additional tools:
- samtools: 0.1.18 (via conda, used by srst2)
- samtools: 1.19 (available as
samtools-1.19) - srst2: 0.2.0
- bowtie2: 2.5.1
- freebayes: 1.3.6
- ncbi-blast+: 2.14.0
- bedtools: 2.31.0
- prodigal: 2.6.3
Basic information on how to use this tool:
- executable:
SPN_Serotyper.pl - help: run with no arguments
- description: Types Streptococcus pneumoniae isolates from paired-end Illumina reads, calling serotype and pilus island using srst2 and freebayes against a curated reference database
Additional information:
Container includes the full SPN_Reference_DB from the Spn_Scripts_Reference repository (commit 2585414), which contains pre-built bowtie2 indexes and FASTA databases for serotyping, resistance typing, and MLST. The reference database is located at /Spn_Scripts_Reference/SPN_Reference_DB/.
Full documentation: https://github.com/BenJamesMetcalf/Spn_Scripts_Reference
SPN_Serotyper.pl \
-1 sample_R1.fastq \
-2 sample_R2.fastq \
-r /Spn_Scripts_Reference/SPN_Reference_DB/SPN_Sero_Gene-DB_Final.fasta \
-o output_dir \
-n sample_name