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Usage: emirge.py DIR <required_parameters> [options]
This version of EMIRGE (emirge.py) attempts to reconstruct rRNA SSU genes from
Illumina metagenomic data.
DIR is the working directory to process data in.
Use --help to see a list of required and optional arguments
Additional information:
https://groups.google.com/group/emirge-users
https://github.com/csmiller/EMIRGE/wiki
If you use EMIRGE in your work, please cite these manuscripts, as appropriate.
Miller CS, Baker BJ, Thomas BC, Singer SW, Banfield JF (2011)
EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data.
Genome biology 12: R44. doi:10.1186/gb-2011-12-5-r44.
Miller CS, Handley KM, Wrighton KC, Frischkorn KR, Thomas BC, Banfield JF (2013)
Short-Read Assembly of Full-Length 16S Amplicons Reveals Bacterial Diversity in Subsurface Sediments.
PloS one 8: e56018. doi:10.1371/journal.pone.0056018.
Options:
-h, --help show this help message and exit
Required flags:
These flags are all required to run EMIRGE, and may be supplied in any
order.
-1 reads_1.fastq[.gz]
path to fastq file with \1 (forward) reads from
paired-end sequencing run, or all reads from single-
end sequencing run. File may optionally be gzipped.
EMIRGE expects ASCII-offset of 64 for quality scores.
(Note that running EMIRGE with single-end reads is
largely untested. Please let me know how it works for
you.)
-f FASTA_DB, --fasta_db=FASTA_DB
path to fasta file of candidate SSU sequences
-b BOWTIE_DB, --bowtie_db=BOWTIE_DB
precomputed bowtie index of candidate SSU sequences
(path to appropriate prefix; see --fasta_db)
-l MAX_READ_LENGTH, --max_read_length=MAX_READ_LENGTH
length of longest read in input data.
Required flags for paired-end reads:
These flags are required to run EMIRGE when you have paired-end reads
(the standard way of running EMIRGE), and may be supplied in any
order.
-2 reads_2.fastq path to fastq file with \2 (reverse) reads from
paired-end run. File must be unzipped for mapper.
EMIRGE expects ASCII-offset of 64 for quality scores.
-i INSERT_MEAN, --insert_mean=INSERT_MEAN
insert size distribution mean.
-s INSERT_STDDEV, --insert_stddev=INSERT_STDDEV
insert size distribution standard deviation.
Optional parameters:
Defaults should normally be fine for these options in order to run
EMIRGE
-n ITERATIONS, --iterations=ITERATIONS
Number of iterations to perform. It may be necessary
to use more iterations for more complex samples
(default=40)
-a PROCESSORS, --processors=PROCESSORS
Number of processors to use in the mapping steps. You
probably want to raise this if you have the
processors. (default: 1)
-m MAPPING, --mapping=MAPPING
path to precomputed initial mapping (bam file). If
not provided, and initial mapping will be run for you.
-p SNP_FRACTION_THRESH, --snp_fraction_thresh=SNP_FRACTION_THRESH
If fraction of variants in a candidate sequence
exceeds this threhold, then split the candidate into
two sequences for next iteration. See also
--variant_fraction_thresh. (default: 0.04)
-v VARIANT_FRACTION_THRESH, --variant_fraction_thresh=VARIANT_FRACTION_THRESH
minimum probability of second most probable base at a
site required in order to call site a variant. See
also --snp_fraction_thresh. (default: 0.1)
-j JOIN_THRESHOLD, --join_threshold=JOIN_THRESHOLD
If two candidate sequences share >= this fractional
identity over their bases with mapped reads, then
merge the two sequences into one for the next
iteration. (default: 0.97; valid range: [0.95, 1.0] )
-c MIN_DEPTH, --min_depth=MIN_DEPTH
minimum average read depth below which a candidate
sequence is discarded for next iteration(default: 3)
--nice_mapping=NICE_MAPPING
If set, during mapping phase, the mapper will be
"niced" by the Linux kernel with this value (default:
no nice)
--phred33 Illumina quality values in fastq files are the (fastq
standard) ascii offset of Phred+33. This is the new
default for Illumina pipeline >= 1.8. DEFAULT is still
to assume that quality scores are Phred+64
-e SAVE_EVERY, --save_every=SAVE_EVERY
every SAVE_EVERY iterations, save some information
about the program's state. This is solely for
debugging information, and is NOT required to resume a
run (see --resume_from below). (default=none)
Resuming iterations:
These options allow you to resume iterations from a previously
completed EMIRGE iteration. This requires that directories for the
iteration to resume from and the previous iteration both be present.
It is STRONGLY recommended that other options set on the command line
be identical to the original run. Note that EMIRGE does not check
this for you!
-r RESUME_FROM, --resume_from=RESUME_FROM
Resume iterations from COMPLETED iteration specified.
Requires that the iteration and previous iteration
fully completed, i.e. a priors file, bam file, and
fasta file are all present in the iteration directory.