BOL

urbe@urbo214b[genome] graphmap align -h []
GraphMap - A very accurate and sensitive long-read, high error-rate sequence mapper
GraphMap Version: v0.5.2
Build date: Jun 6 2017 at 15:45:57

GraphMap (c) by Ivan Sovic, Mile Sikic and Niranjan Nagarajan
GraphMap is licensed under The MIT License.

Affiliations: Ivan Sovic (1, 3), Mile Sikic (2), Niranjan Nagarajan (3)
(1) Ruder Boskovic Institute, Zagreb, Croatia
(2) University of Zagreb, Faculty of Electrical Engineering and Computing
(3) Genome Institute of Singapore, A*STAR, Singapore

Usage:
graphmap [options] -r <reference_file> -d <reads_file> -o <output_sam_path>

Usage:
graphmap [options]

Options
Input/Output options:
-r, --ref STR Path to the reference sequence (fastq or fasta).
-i, --index STR Path to the index of the reference sequence. If not specified, index is generated in
the same folder as the reference file, with .gmidx extension. For non-parsimonious
mode, secondary index .gmidxsec is also generated.
-d, --reads STR Path to the reads file.
-o, --out STR Path to the output file that will be generated.
--gtf STR Path to a General Transfer Format file. If specified, a transcriptome will be built
from the reference sequence and used for mapping. Output SAM alignments will be in
genome space (not transcriptome).
-K, --in-fmt STR Format in which to input reads. Options are:
auto - Determines the format automatically from file extension.
fastq - Loads FASTQ or FASTA files.
fasta - Loads FASTQ or FASTA files.
gfa - Graphical Fragment Assembly format.
sam - Sequence Alignment/Mapping format. [auto]
-L, --out-fmt STR Format in which to output results. Options are:
sam - Standard SAM output (in normal and '-w overlap' modes).
m5 - BLASR M5 format. [sam]
-I, --index-only - Build only the index from the given reference and exit. If not specified, index will
automatically be built if it does not exist, or loaded from file otherwise. [false]
--rebuild-index - Always rebuild index even if it already exists in given path. [false]
--auto-rebuild-index - Rebuild index only if an existing index is of an older version or corrupt. [false]
-u, --ordered - SAM alignments will be output after the processing has finished, in the order of
input reads. [false]
-B, --batch-mb INT Reads will be loaded in batches of the size specified in megabytes. Value <= 0 loads
the entire file. [1024]

General-purpose pre-set options:
-x, --preset STR Pre-set parameters to increase sensitivity for different sequencing technologies.
Valid options are:
illumina - Equivalent to: '-a gotoh -w normal -M 5 -X 4 -G 8 -E 6'
overlap - Equivalent to: '-a anchor -w normal --overlapper --evalue 1e0
--ambiguity 0.50 --secondary'
sensitive - Equivalent to: '--freq-percentile 1.0 --minimizer-window 1'

Alignment options:
-a, --alg STR Specifies which algorithm should be used for alignment. Options are:
sg - Myers' bit-vector approach. Semiglobal. Edit dist. alignment.
sggotoh - Gotoh alignment with affine gaps. Semiglobal.
anchor - anchored alignment with end-to-end extension.
Uses Myers' global alignment to align between anchors.
anchorgotoh - anchored alignment with Gotoh.
Uses Gotoh global alignment to align between anchors. [anchor]
-w, --approach STR Additional alignment approaches. Changes the way alignment algorithm is applied.
Options are:
normal - Normal alignment of reads to the reference.
(Currently no other options are provided. This is a placeholder for future features,
such as cDNA mapping) [normal]
--overlapper - Perform overlapping instead of mapping. Skips self-hits if reads and reference files
contain same sequences, and outputs lenient secondary alignments. [false]
--no-self-hits - Similar to overlapper, but skips mapping of sequences with same headers. Same
sequences can be located on different paths, and their overlap still skipped. [false]
-M, --match INT Match score for the DP alignment. Ignored for Myers alignment. [5]
-X, --mismatch INT Mismatch penalty for the DP alignment. Ignored for Myers alignment. [4]
-G, --gapopen INT Gap open penalty for the DP alignment. Ignored for Myers alignment. [8]
-E, --gapext INT Gap extend penalty for the DP alignment. Ignored for Myers alignment. [6]
-z, --evalue FLT Threshold for E-value. If E-value > FLT, read will be called unmapped. If FLT < 0.0,
thredhold not applied. [1e0]
-c, --mapq INT Threshold for mapping quality. If mapq < INT, read will be called unmapped. [1]
--extcigar - Use the extended CIGAR format for output alignments. [false]
--no-end2end - Disables extending of the alignments to the ends of the read. Works only for
anchored modes. [false]
--max-error FLT If an alignment has error rate (X+I+D) larger than this, it won't be taken into
account. If >= 1.0, this filter is disabled. [1.0]
--max-indel-error FLT If an alignment has indel error rate (I+D) larger than this, it won't be taken into
account. If >= 1.0, this filter is disabled. [1.0]

Algorithmic options:
-k INT Graph construction kmer size. [6]
-l INT Number of edges per vertex. [9]
-A, --minbases INT Minimum number of match bases in an anchor. [12]
-e, --error-rate FLT Approximate error rate of the input read sequences. [0.45]
-g, --max-regions INT If the final number of regions exceeds this amount, the read will be called
unmapped. If 0, value will be dynamically determined. If < 0, no limit is set. [0]
-q, --reg-reduce INT Attempt to heuristically reduce the number of regions if it exceeds this amount.
Value <= 0 disables reduction but only if param -g is not 0. If -g is 0, the value of
this parameter is set to 1/5 of maximum number of regions. [0]
-C, --circular - Reference sequence is a circular genome. [false]
-F, --ambiguity FLT All mapping positions within the given fraction of the top score will be counted for
ambiguity (mapping quality). Value of 0.0 counts only identical mappings. [0.02]
-Z, --secondary - If specified, all (secondary) alignments within (-F FLT) will be output to a file.
Otherwise, only one alignment will be output. [false]
-P, --double-index - If false, only one gapped spaced index will be used in region selection. If true,
two such indexes (with different shapes) will be used (2x memory-hungry but more
powerful for very high error rates). [false]
--min-bin-perc FLT Consider only bins with counts above FLT * max_bin, where max_bin is the count of
the top scoring bin. [0.75]
--bin-step FLT After a chunk of bins with values above FLT * max_bin is processed, check if there
is one extremely dominant region, and stop the search. [0.25]
--min-read-len INT If a read is shorter than this, it will be marked as unmapped. This value can be
lowered if the reads are known to be accurate. [80]
--minimizer-window INT Length of the window to select a minimizer from. If equal to 1, minimizers will be
turned off. [5]
--freq-percentile FLT Filer the (1.0 - value) percent of most frequent seeds in the lookup process. [0.99]
--fly-index - Index will be constructed on the fly, without storing it to disk. If it already
exists on disk, it will be loaded unless --rebuild-index is specified. [false]

Other options:
-t, --threads INT Number of threads to use. If '-1', number of threads will be equal to min(24, num_cores/2). [-1]
-v, --verbose INT Verbose level. If equal to 0 nothing except strict output will be placed on stdout. [5]
-s, --start INT Ordinal number of the read from which to start processing data. [0]
-n, --numreads INT Number of reads to process per batch. Value of '-1' processes all reads. [-1]
-h, --help - View this help. [false]

Debug options:
-y, --debug-read INT ID of the read to give the detailed verbose output. [-1]
-Y, --debug-qname STR QNAME of the read to give the detailed verbose output. Has precedence over -y. Use
quotes to specify.
-b, --verbose-sam INT Helpful debug comments can be placed in SAM output lines (at the end). Comments can
be turned off by setting this parameter to 0. Different values increase/decrease
verbosity level.
0 - verbose off
1 - server mode, command line will be omitted to obfuscate paths.
2 - umm this one was skipped by accident. The same as 0.
>=3 - detailed verbose is added for each alignment, including timing measurements and
other.
4 - qnames and rnames will not be trimmed to the first space.
5 - QVs will be omitted (if available). [0]