Whole-genome sequencing quality control and assembly pipeline
If you found the fsl_wgs_pipeline, its source code, and/or any of its associated databases useful, please cite:
Carroll, Laura M. 2019. fsl_wgs_pipeline: Whole-genome sequencing quality control and assembly. Version 1.0.0. https://github.com/lmc297/fsl_wgs_pipeline.
usage: fsl_wgs_pipeline -i </path/to/list/of/isolate/file/paths.txt> -o </path/to/output/directory/> [-other options]
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
Path to tab-separated list of isolate file paths and
names, one isolate per line; paired-end reads should
have the path to forward reads, path to reverse reads,
and the desired isolate name, each separated by a tab,
while single-end reads should have the path to the
reads and the desired isolate name, separated by a tab
-o OUTPUT, --output OUTPUT
Path to desired output directory
--threads [THREADS] Optional argument; integer; number of threads; default
= 1
--fastqc_path [FASTQC_PATH]
Optional argument for use with --trimmed_fastqc True;
fastqc, unless path to fastqc is supplied; path to
fastqc; default = fastqc (fastqc is in your path)
--multiqc [MULTIQC] Optional argument; True or False; run multiqc on reads
and/or assemblies; default = True
--multiqc_path [MULTIQC_PATH]
Optional argument; multiqc or path to multiqc; path to
multiqc; default = multiqc (multiqc is in the user's
path
--trimmer [TRIMMER] Optional argument; trimmomatic or False; trim reads
using trimmomatic or skip read trimming (--trimmer
False); default = trimmomatic
--trimmomatic_jar [TRIMMOMATIC_JAR]
Argument for use with --trimmer trimmomatic;
trimmomatic-0.39.jar, unless path to trimmomatic jar
file is supplied; path to trimmomatic jar file (named
trimmomatic-version.jar); default =
trimmomatic-0.39.jar (jar for trimmomatic version 0.39
is in your path)
--trimmomatic_adapters [TRIMMOMATIC_ADAPTERS]
Argument for use with --trimmer trimmomatic; False,
unless path to trimmomatic adapter sequences is
supplied; path to trimmomatic adapter sequences;
default = False (no path supplied)
--trimmomatic_phred [TRIMMOMATIC_PHRED]
Optional argument for use with --trimmer trimmomatic;
phred33 or phred64; specify phred quality encoding of
fastq files to be trimmed (note that this should not
be changed unless working with very, very old Illumina
data); default = phred33
--trimmomatic_illuminaclip [TRIMMOMATIC_ILLUMINACLIP]
Optional argument for use with --trimmer trimmomatic;
integer:integer:integer; ILLUMINACLIP seed mismatches
(specifies the maximum mismatch count which will still
allow a full match to be performed), palindrome clip
threshold (specifies how accurate the match between
the two 'adapter ligated' reads must be for PE
palindrome read alignment), and simple clip threshold
(specifies how accurate the match between any adapter
etc. sequence must be against a read), each separated
by a colon (<seed mismatches>:<palindrome clip
threshold>:<simple clip threshold>); default = 2:30:10
--trimmomatic_leading [TRIMMOMATIC_LEADING]
Optional argument for use with --trimmer trimmomatic;
integer; argument to pass to trimmomatic's LEADING
argument (cut bases off the start of a read, if below
a threshold quality); default = 3
--trimmomatic_trailing [TRIMMOMATIC_TRAILING]
Optional argument for use with --trimmer trimmomatic;
integer; argument to pass to trimmomatic's TRAILING
argument (cut bases off the end of a read, if below a
threshold quality); default = 3
--trimmomatic_slidingwindow [TRIMMOMATIC_SLIDINGWINDOW]
Optional argument for use with --trimmer trimmomatic;
integer:integer; SLIDINGWINDOW window size (specifies
the number of bases to average across) and required
quality (specifies the average quality required),
separated by a colon (<window size>:<required
quality>); default = 4:15
--trimmomatic_minlen [TRIMMOMATIC_MINLEN]
Optional argument for use with --trimmer trimmomatic;
integer; argument to pass to trimmomatic's MINLEN
argument (drop the read if it is below a specified
length); default = 36
--trimmed_fastqc [TRIMMED_FASTQC]
Optional argument for use with --trimmer trimmomatic;
True or False; run fastqc on trimmed Illumina reads;
default = True
--assembler [ASSEMBLER]
Optional argument; spades or False; assemble genome
with spades or skip assembly (--assembler False);
default = spades
--spades_path [SPADES_PATH]
Argument for use with --assembler spades; spades.py,
unless path to spades.py is supplied; path to
spades.py; default = spades.py (spades.py is in the
user's path)
--spades_m [SPADES_M]
Optional argument for use with --assembler spades;
integer; memory limit for spades in Gb (spades
terminates if it reaches this limit); default = 20
--min_contig_length [MIN_CONTIG_LENGTH]
Optional argument for use with --assembler spades;
integer; remove contigs less than specified length (in
bp) from each assembly (note that this only applies to
'final' assemblies copied into the 'contigs' directory
in the 'fsl_wgs_pipeline_final_results' directory; all
original, unfiltered assemblies are unchanged and
remain in the isolate's respective directory in the
'spades_output' directory in the
'fsl_wgs_pipeline_final_results' directory; default =
200
--quast [QUAST] Optional argument for use with --assembler spades;
True or False; run quast on assembled genomes; default
= True
--quast_path [QUAST_PATH]
Argument for use with --quast True; quast.py, unless
path to quast.py is supplied; path to quast.py;
default = quast.py (quast.py is in the user's path)
--quast_min_contig [QUAST_MIN_CONTIG]
Optional argument for use with --quast True; integer;
--min-contig threshold for quast contig length to
consider (in bp; shorter contigs won't be taken into
account, except for specific metrics); default = 1
(quast considers all contigs)
--coverage [COVERAGE]
Optional argument for use with --assembler spades;
True or False; calculate coverage of assembly by
mapping reads back to assembly using bwa/samtools;
default = True
--bwa_path [BWA_PATH]
Argument for use with --coverage True; bwa, unless
path to bwa is supplied; path to bwa; default = bwa
(bwa is in the user's path)
--samtools_path [SAMTOOLS_PATH]
Argument for use with --coverage True; samtools,
unless path to samtools is supplied; path to samtools;
default = samtools (samtools is in the user's path)
--version Print version
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