virseaqc - A combined pipeline for VIRal genome SEarching, Assembly, and Quality Control on Ion-Torrent instruments.
usage: virseaqc [-h] -q READS_DIR -o OUTDIR [-b DB] [-s HOST_GENOME]
[-a ADAPTERS] [-t THREADS] [-p] [-i] [-m MEM] [-f] [--version]
[-v]
virseaqc - A combined pipeline for VIRal genome SEarching, Assembly, and
Quality Control on Ion-Torrent instruments.
required arguments:
-q READS_DIR, --fastq-dir READS_DIR
Path to a directory with your ion-torrent or single
end fastq files.
-o OUTDIR, --output-directory OUTDIR
Path to the output directory. A directory will be
created if one does not exist.
-b DB, --blast_database DB
Path to the local nt blast database. This pipeline
requires you to have a local copy of the nt database.
See https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&P
AGE_TYPE=BlastDocs&DOC_TYPE=Download to install a
local nt database.
-s HOST_GENOME, --host_genome HOST_GENOME
Path to the host reference genome to remove host reads
-a ADAPTERS, --adapters ADAPTERS
Path to the file containing adapter reads for removal
from sequence reads
optional arguments:
-h, --help show this help message and exit
-t THREADS, --threads THREADS
Number of threads to use for multiprocessing.
-p, --paired_end Reads are sourced from an Illumina instrument rather
than an Ion Torrent and are paired-end. Note that
these files must end with n.fastq(.gz), where n=1,2
-i, --interleaved Reads are sourced from an Illumina instrument rather
than an Ion Torrent and are paired-end interleaved.
-m MEM, --max_memory MEM
Maximum amount of RAM to assign to the pipeline in GB
(Just the number).
-f, --force Overwrite files in the output directories.
--version show program's version number and exit
-v, --verbose Increase verbosity on command line output (n.b.
verbose output is always saved to virseaqc.log in the
output directory).