Provided by: gmap_2011-11-30-1_amd64
gsnap - Genomic Short-read Nucleotide Alignment Program
gsnap -dDB [OPTION]... [QUERY]...
Align the sequences QUERY to the reference DB. With no QUERY, read standard input.
Input options -D, --dir=directory Genome directory -d, --db=STRING Genome database -k, --kmer=INT kmer size to use in genome database (allowed values: 12-15). If not specified, the program will find the highest available kmer size in the genome database -q, --part=INT/INT Process only the i-th out of every n sequences e.g., 0/100 or 99/100 (useful for distributing jobs to a computer farm). --input-buffer=INT Size of input buffer (program reads this many sequences at a time for efficiency) (default 1000) --barcode-length=INT Amount of barcode to remove from start of read (default 0) -o, --orientation=STRING Orientation of paired-end reads Allowed values: FR (fwd-rev, or typical Illumina; default), RF (rev-fwd, for circularized inserts), or FF (fwd-fwd, same strand) --fastq-id-start=INT Starting position of identifier in FASTQ header, space-delimited (>= 1) --fastq-id-end=INT Ending position of identifier in FASTQ header, space-delimited (>= 1) Examples: @HWUSI-EAS100R:6:73:941:1973#0/1 start=1, end=1 (default) => identifier is HWUSI-EAS100R:6:73:941:1973#0 @SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=36 start=1, end=1 => identifier is SRR001666.1 start=2, end=2 => identifier is 071112_SLXA-EAS1_s_7:5:1:817:345 start=1, end=2 => identifier is SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 --filter-chastity=STRING Skips reads marked by the Illumina chastity program. Expecting a string after the accession having a 'Y' after the first colon, like this: @accession 1:Y:0:CTTGTA where the 'Y' signifies filtering by chastity. Values: off (default), either, both. For 'either', a 'Y' on either end of a paired-end read will be filtered. For 'both', a 'Y' is required on both ends of a paired-end read (or on the only end of a single-end read). Computation options Note: GSNAP has an ultrafast algorithm for calculating mismatches up to and including ((readlength+2)/kmer - 2) ("ultrafast mismatches"). The program will run fastest if max-mismatches (plus suboptimal-levels) is within that value. Also, indels, especially end indels, take longer to compute, although the algorithm is still designed to be fast. -B, --batch=INT Mode Offsets Positions Genome 0 allocate mmap mmap 1 allocate mmap & preload mmap 2 allocate mmap & preload mmap & preload (default) 3 allocate allocate mmap & preload 4 allocate allocate allocate 5 expand allocate allocate Note: For a single sequence, all data structures use mmap. If mmap not available and allocate not chosen, then will use fileio (very slow) -m, --max-mismatches=FLOAT Maximum number of mismatches allowed (if not specified, then defaults to the ultrafast level of ((readlength+2)/kmer - 2)) If specified between 0.0 and 1.0, then treated as a fraction of each read length. Otherwise, treated as an integral number of mismatches (including indel and splicing penalties) For RNA-Seq, you may need to increase this value slightly to align reads extending past the ends of an exon. --query-unk-mismatch=INT Whether to count unknown (N) characters in the query as a mismatch (0=no (default), 1=yes) --genome-unk-mismatch=INT Whether to count unknown (N) characters in the genome as a mismatch (0=no, 1=yes (default)) --terminal-threshold=INT Threshold for searching for a terminal alignment (from one end of the read to the best possible position at the other end) (default 2). For example, if this value is 2, then if GSNAP finds an exact or 1-mismatch alignment, it will not try to find a terminal alignment. Note that this default value may not be low enough if you want to obtain terminal alignments for very short reads, although such reads probably don't have enough specificity for terminal alignments anyway. To turn off terminal alignments, set this to a high value, greater than the value for --max- mismatches. -i, --indel-penalty=INT Penalty for an indel (default 2). Counts against mismatches allowed. To find indels, make indel-penalty less than or equal to max-mismatches. A value < 2 can lead to false positives at read ends --indel-endlength=INT Minimum length at end required for indel alignments (default 4) -y, --max-middle-insertions=INT Maximum number of middle insertions allowed (default 9) -z, --max-middle-deletions=INT Maximum number of middle deletions allowed (default 30) -Y, --max-end-insertions=INT Maximum number of end insertions allowed (default 3) -Z, --max-end-deletions=INT Maximum number of end deletions allowed (default 6) -M, --suboptimal-levels=INT Report suboptimal hits beyond best hit (default 0) All hits with best score plus suboptimal-levels are reported -a, --adapter-strip=STRING Method for removing adapters from reads. Currently allowed values: off, paired. Default is "paired", which removes adapters from paired-end reads if a concordant or paired alignment cannot be found from the original read. To turn off, use the value "off". --trim-mismatch-score=INT Score to use for mismatches when trimming at ends (default is -3; to turn off trimming, specify 0). Warning: turning trimming off will give false positive mismatches at the ends of reads --trim-indel-score=INT Score to use for indels when trimming at ends (default is -4; to turn off trimming, specify 0). Warning: turning trimming off will give false positive indels at the ends of reads -V, --snpsdir=STRING Directory for SNPs index files (created using snpindex) (default is location of genome index files specified using -D and -d) -v, --use-snps=STRING Use database containing known SNPs (in <STRING>.iit, built previously using snpindex) for tolerance to SNPs --cmetdir=STRING Directory for methylcytosine index files (created using cmetindex) default is location of genome index files specified using -D, -V, and -d) --atoidir=STRING Directory for A-to-I RNA editing index files (created using atoiindex) (default is location of genome index files specified using -D, -V, and -d) --mode=STRING Alignment mode: standard (default), cmet-stranded, cmet-nonstranded, atoi-stranded, or atoi-nonstranded. Non-standard modes requires you to have previously run the cmetindex or atoiindex programs on the genome --tallydir=STRING Directory for tally IIT file to resolve concordant multiple results (default is location of genome index files specified using -D and -d). Note: can just give full path name to --use-tally instead. --use-tally=STRING Use this tally IIT file to resolve concordant multiple results --runlengthdir=STRING Directory for runlength IIT file to resolve concordant multiple results (default is location of genome index files specified using -D and -d). Note: can just give full path name to --use-runlength instead. --use-runlength=STRING Use this runlength IIT file to resolve concordant multiple results -t, --nthreads=INT Number of worker threads Options for GMAP alignment within GSNAP --gmap-mode=STRING Cases to use GMAP for complex alignments containing multiple splices or indels. Allowed values: none, pairsearch, terminal, improve (or multiple, separated by commas). Default: pairsearch,terminal,improve --trigger-score-for-gmap=INT Try GMAP pairsearch on nearby genomic regions if best score (the total of both ends if paired-end) exceeds this value (default 5) --max-gmap-pairsearch=INT Perform GMAP pairsearch on nearby genomic regions up to this many many candidate ends (default 3). Requires pairsearch in --gmap-mode --max-gmap-terminal=INT Perform GMAP terminal on nearby genomic regions up to this many candidate ends (default 3). Requires terminal in --gmap-mode --max-gmap-improvement=INT Perform GMAP improvement on nearby genomic regions up to this many --microexon-spliceprob=FLOAT Allow microexons only if one of the splice site probabilities is greater than this value (default 0.90) Splicing options for RNA-Seq -N, --novelsplicing=INT Look for novel splicing (0=no (default), 1=yes) --splicingdir=STRING Directory for splicing involving known sites or known introns, as specified by the -s or --use-splicing flag (default is directory computed from -D and -d flags). Note: can just give full pathname to the -s flag instead. -s, --use-splicing=STRING Look for splicing involving known sites or known introns (in <STRING>.iit), at short or long distances. See README instructions for the distinction between known sites and known introns --ambig-splice-noclip For ambiguous known splicing at ends of the read, do not clip at the splice site, but extend instead into the intron. This flag makes sense only if you provide the --use-splicing flag, and you are trying to eliminate all soft clipping with --trim- mismatch-score=0 -w, --localsplicedist=INT Definition of local novel splicing event (default 200000) -e, --local-splice-penalty=INT Penalty for a local splice (default 0). Counts against mismatches allowed -E, --distant-splice-penalty=INT Penalty for a distant splice (default 3). A distant splice is one where the intron length exceeds the value of -w, or --localsplicedist, or is an inversion, scramble, or translocation between two different chromosomes Counts against mismatches allowed -K, --distant-splice-endlength=INT Minimum length at end required for distant spliced alignments (default 16, min allowed is the value of -k, or kmer size) -l, --shortend-splice-endlength=INT Minimum length at end required for short-end spliced alignments (default 2) but unless known splice sites are provided with the -s flag, GSNAP may still need the end length to be the value of -k, or kmer size to find a given splice --distant-splice-identity=FLOAT Minimum identity at end required for distant spliced alignments (default 0.95) --antistranded-penalty=INT Penalty for antistranded splicing when using stranded RNA-Seq protocols. A positive value, such as 1, expects antisense on the first read and sense on the second read. Default is 0, which treats sense and antisense equally well --merge-distant-samechr Report distant splices on the same chromosome as a single splice, if possible. Will produce a single SAM line instead of two SAM lines, which is also done for translocations, inversions, and scramble events Options for paired-end reads --pairmax-dna=INT Max total genomic length for DNA-Seq paired reads, or other reads without splicing (default 1000). Used if -N or -s is not specified. --pairmax-rna=INT Max total genomic length for RNA-Seq paired reads, or other reads that could have a splice (default 200000). Used if -N or -s is specified. Should probably match the value for -w, --localsplicedist. --pairexpect=INT Expected paired-end length, used for calling splices in medial part of paired-end reads (default 200) --pairdev=INT Allowable deviation from expected paired-end length, used for calling splices in medial part of paired-end reads (default 25) Options for quality scores --quality-protocol=STRING Protocol for input quality scores. Allowed values: illumina (ASCII 64-126) (equivalent to -J 64 -j -31) sanger (ASCII 33-126) (equivalent to -J 33 -j 0) Default is sanger (no quality print shift) SAM output files should have quality scores in sanger protocol Or you can customize this behavior with these flags: -J, --quality-zero-score=INT FASTQ quality scores are zero at this ASCII value (default is 33 for sanger protocol; for Illumina, select 64) -j, --quality-print-shift=INT Shift FASTQ quality scores by this amount in output (default is 0 for sanger protocol; to change Illumina input to Sanger output, select -31) Output options -n, --npaths=INT Maximum number of paths to print (default 100). -Q, --quiet-if-excessive If more than maximum number of paths are found, then nothing is printed. -O, --ordered Print output in same order as input (relevant only if there is more than one worker thread) --show-refdiff For GSNAP output in SNP-tolerant alignment, shows all differences relative to the reference genome as lower case (otherwise, it shows all differences relative to both the reference and alternate genome) --clip-overlap For paired-end reads whose alignments overlap, clip the overlapping region. --print-snps Print detailed information about SNPs in reads (works only if -v also selected) (not fully implemented yet) --failsonly Print only failed alignments, those with no results --nofails Exclude printing of failed alignments --fails-as-input=STRING Print completely failed alignments as input FASTA or FASTQ format Allowed values: yes, no -A, --format=STRING Another format type, other than default. Currently implemented: sam Also allowed, but not installed at compile-time: goby (To install, need to re-compile with appropriate options) --output-buffer-size=INT Buffer size, in queries, for output thread (default 1000). When the number of results to be printed exceeds this size, the worker threads are halted until the backlog is cleared Options for SAM output --no-sam-headers Do not print headers beginning with '@' --sam-headers-batch=INT Print headers only for this batch, as specified by -q --read-group-id=STRING Value to put into read-group id (RG-ID) field --read-group-name=STRING Value to put into read-group name (RG-SM) field --read-group-library=STRING Value to put into read-group library (RG-LB) field --read-group-platform=STRING Value to put into read-group library (RG-PL) field Help options --version Show version --help Show this help message
GMAPDB genome directory (eqivalent to -D)
~/.gmaprc configuration file
Thomas D. Wu and Colin K. Watanabe
Report bugs to Thomas Wu <email@example.com>.
Copyright 2005 Genentech, Inc. All rights reserved.