Genome assembly and Variant Calling for Polyoma BK Virus (PyBKV).
To install the pipeline just:
git clone https://github.com/joanmarticarreras/BKAnaLite
cd BKAnaLite
./BKAnaLite.sh --help
BKAnaLite depends on a series of dependencies, which executables should be in $PATH:
BBMap
IVA
BLAST
SeqTK
Python2.7
Python3
BWA
SAMTools
LoFreq
bgzip
tabix
bcftools
RATT
Additionally, BKAnaLite depends on the script circules.py from the MITObim package. Accessory scripts from RATT should be in $PATH too (NOTE: Depend on Python2.7).
Absolute paths to RATT and the annotated reference genome in EMBL format should be added in L209. Path to a file containing the sequencing adapters and PCR primers (if used) should be added in L80.
Usage: BKAnaLite.sh [OPTIONS]
-r Path to reference genome in FASTA format
-1 Path to R1 Illunmina PE reads
-2 Path to R2 Illumina PE reads
-s Path to Sanger reads in FASTQ format
-t Number of threads to use when multithreading is possible
-x Basename for the output files
-o Path to output directory
-h help (this output)