razers3 (1)

Faster, fully sensitive read mapping synopsis razers3 [options] genome file reads file razers3 [options] genome file pe-reads file1 pe-reads file2 description razers 3 is a versatile full-sensitive read mapper based on k-mer counting and seeding filters. it supports single and paired-end mapping, shared-memory parallelism, and optimally parametrizes the filter based on a user-defined minimal sensitivity. see http://www.seqan.de/projects/razers for more information. input to razers 3 is a reference genome file and either one file with single-end reads or two files containing left or right mates of paired-end reads. (c) copyright 2009-2013 by david weese. -h, --help displays this help message. --version display version information main options: -i, --percent-identity num percent identity threshold. in range [50..100]. default: 95. -rr, --recognition-rate num percent recognition rate. in range [80..100]. default: 99. -ng, --no-gaps allow only mismatches, no indels. default: allow both. -f, --forward map reads only to forward strands. -r, --reverse map reads only to reverse strands. -m, --max-hits num output only num of the best hits. in range [1..inf]. default: 100. --unique output only unique best matches (-m 1 -dr 0 -pa). -tr, --trim-reads num trim reads to given length. default: off. in range [14..inf]. -o, --output file mapping result filename. default: reads file.razers. valid filetypes are: .razers, .eland, .fa, .fasta, .gff, .sam, and .afg. -v, --verbose verbose mode. -vv, --vverbose very verbose mode. paired-end options: -ll, --library-length num paired-end library length. in range [1..inf]. default: 220. -le, --library-error num paired-end library length tolerance. in range [0..inf]. default: 50. output format options: -a, --alignment dump the alignment for each match (only razer or fasta format). -pa, --purge-ambiguous purge reads with more than max-hits best matches. -dr, --distance-range num only consider matches with at most num more errors compared to the best. default: output all. -gn, --genome-naming num select how genomes are named (see naming section below). in range [0..1]. default: 0. -rn, --read-naming num select how reads are named (see naming section below). in range [0..3]. default: 0. --full-readid use the whole read id (don't clip after whitespace). -so, --sort-order num select how matches are sorted (see sorting section below). in range [0..1]. default: 0. -pf, --position-format num select begin/end position numbering (see coordinate section below). in range [0..1]. default: 0. -ds, --dont-shrink-alignments disable alignment shrinking in sam. this is required for generating a gold mapping for rabema. filtration options: -fl, --filter str select k-mer filter. one of pigeonhole and swift. default: pigeonhole. -mr, --mutation-rate num set the percent mutation rate (pigeonhole). in range [0..20]. default: 5. -ol, --overlap-length num manually set the overlap length of adjacent k-mers (pigeonhole). in range [0..inf]. -pd, --param-dir dir read user-computed parameter files in the directory dir (swift). -t, --threshold num manually set minimum k-mer count threshold (swift). in range [1..inf]. -tl, --taboo-length num set taboo length (swift). in range [1..inf]. default: 1. -s, --shape bitstring manually set k-mer shape. -oc, --overabundance-cut num set k-mer overabundance cut ratio. in range [0..1]. default: 1. -rl, --repeat-length num skip simple-repeats of length num. in range [1..inf]. default: 1000. -lf, --load-factor num set the load factor for the open addressing k-mer index. in range [1..inf]. default: 1.6. verification options: -mn, --match-n n matches all other characters. default: n matches nothing. -ed, --error-distr file write error distribution to file. -mf, --mismatch-file file write mismatch patterns to file. misc options: -cm, --compact-mult num multiply compaction treshold by this value after reaching and compacting. in range [0..inf]. default: 2.2. -ncf, --no-compact-frac num don't compact if in this last fraction of genome. in range [0..1]. default: 0.05. parallelism options: -pws, --parallel-window-size num collect candidates in windows of this length. in range [1..inf]. default: 500000. -pvs, --parallel-verification-size num verify candidates in packages of this size. in range [1..inf]. default: 100. -pvmpc, --parallel-verification-max-package-count num largest number of packages to create for verification per thread-1. in range [1..inf]. default: 100. -amms, --available-matches-memory-size num bytes of main memory available for storing matches. in range [-1..inf]. default: 0. -mhst, --match-histo-start-threshold num when to start histogram. in range [1..inf]. default: 5. formats, naming, sorting, and coordinate schemes razers 3 supports various output formats. the output format is detected automatically from the file name suffix. .razers razer format .fa, .fasta enhanced fasta format .eland eland format

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  4. razers3: Faster, fully sensitive read mapping synopsis razers3 [options] genome file reads file razers3 [options] genome file pe-reads file1 pe-reads file2 description razers 3 is a versatile full-sensitive read mapper based on k-mer counting and seeding filters. it supports single and paired-end mapping, shared-memory parallelism, and optimally parametrizes the filter based on a user-defined minimal sensitivity. see http://www.seqan.de/projects/razers for more information. input to razers 3 is a reference genome file and either one file with single-end reads or two files containing left or right mates of paired-end reads. (c) copyright 2009-2013 by david weese. -h, --help displays this help message. --version display version information main options: -i, --percent-identity num percent identity threshold. in range [50..100]. default: 95. -rr, --recognition-rate num percent recognition rate. in range [80..100]. default: 99. -ng, --no-gaps allow only mismatches, no indels. default: allow both. -f, --forward map reads only to forward strands. -r, --reverse map reads only to reverse strands. -m, --max-hits num output only num of the best hits. in range [1..inf]. default: 100. --unique output only unique best matches (-m 1 -dr 0 -pa). -tr, --trim-reads num trim reads to given length. default: off. in range [14..inf]. -o, --output file mapping result filename. default: reads file.razers. valid filetypes are: .razers, .eland, .fa, .fasta, .gff, .sam, and .afg. -v, --verbose verbose mode. -vv, --vverbose very verbose mode. paired-end options: -ll, --library-length num paired-end library length. in range [1..inf]. default: 220. -le, --library-error num paired-end library length tolerance. in range [0..inf]. default: 50. output format options: -a, --alignment dump the alignment for each match (only razer or fasta format). -pa, --purge-ambiguous purge reads with more than max-hits best matches. -dr, --distance-range num only consider matches with at most num more errors compared to the best. default: output all. -gn, --genome-naming num select how genomes are named (see naming section below). in range [0..1]. default: 0. -rn, --read-naming num select how reads are named (see naming section below). in range [0..3]. default: 0. --full-readid use the whole read id (don't clip after whitespace). -so, --sort-order num select how matches are sorted (see sorting section below). in range [0..1]. default: 0. -pf, --position-format num select begin/end position numbering (see coordinate section below). in range [0..1]. default: 0. -ds, --dont-shrink-alignments disable alignment shrinking in sam. this is required for generating a gold mapping for rabema. filtration options: -fl, --filter str select k-mer filter. one of pigeonhole and swift. default: pigeonhole. -mr, --mutation-rate num set the percent mutation rate (pigeonhole). in range [0..20]. default: 5. -ol, --overlap-length num manually set the overlap length of adjacent k-mers (pigeonhole). in range [0..inf]. -pd, --param-dir dir read user-computed parameter files in the directory dir (swift). -t, --threshold num manually set minimum k-mer count threshold (swift). in range [1..inf]. -tl, --taboo-length num set taboo length (swift). in range [1..inf]. default: 1. -s, --shape bitstring manually set k-mer shape. -oc, --overabundance-cut num set k-mer overabundance cut ratio. in range [0..1]. default: 1. -rl, --repeat-length num skip simple-repeats of length num. in range [1..inf]. default: 1000. -lf, --load-factor num set the load factor for the open addressing k-mer index. in range [1..inf]. default: 1.6. verification options: -mn, --match-n n matches all other characters. default: n matches nothing. -ed, --error-distr file write error distribution to file. -mf, --mismatch-file file write mismatch patterns to file. misc options: -cm, --compact-mult num multiply compaction treshold by this value after reaching and compacting. in range [0..inf]. default: 2.2. -ncf, --no-compact-frac num don't compact if in this last fraction of genome. in range [0..1]. default: 0.05. parallelism options: -pws, --parallel-window-size num collect candidates in windows of this length. in range [1..inf]. default: 500000. -pvs, --parallel-verification-size num verify candidates in packages of this size. in range [1..inf]. default: 100. -pvmpc, --parallel-verification-max-package-count num largest number of packages to create for verification per thread-1. in range [1..inf]. default: 100. -amms, --available-matches-memory-size num bytes of main memory available for storing matches. in range [-1..inf]. default: 0. -mhst, --match-histo-start-threshold num when to start histogram. in range [1..inf]. default: 5. formats, naming, sorting, and coordinate schemes razers 3 supports various output formats. the output format is detected automatically from the file name suffix. .razers razer format .fa, .fasta enhanced fasta format .eland eland format
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  4. razers3: Faster, fully sensitive read mapping synopsis razers3 [options] genome file reads file razers3 [options] genome file pe-reads file1 pe-reads file2 description razers 3 is a versatile full-sensitive read mapper based on k-mer counting and seeding filters. it supports single and paired-end mapping, shared-memory parallelism, and optimally parametrizes the filter based on a user-defined minimal sensitivity. see http://www.seqan.de/projects/razers for more information. input to razers 3 is a reference genome file and either one file with single-end reads or two files containing left or right mates of paired-end reads. (c) copyright 2009-2013 by david weese. -h, --help displays this help message. --version display version information main options: -i, --percent-identity num percent identity threshold. in range [50..100]. default: 95. -rr, --recognition-rate num percent recognition rate. in range [80..100]. default: 99. -ng, --no-gaps allow only mismatches, no indels. default: allow both. -f, --forward map reads only to forward strands. -r, --reverse map reads only to reverse strands. -m, --max-hits num output only num of the best hits. in range [1..inf]. default: 100. --unique output only unique best matches (-m 1 -dr 0 -pa). -tr, --trim-reads num trim reads to given length. default: off. in range [14..inf]. -o, --output file mapping result filename. default: reads file.razers. valid filetypes are: .razers, .eland, .fa, .fasta, .gff, .sam, and .afg. -v, --verbose verbose mode. -vv, --vverbose very verbose mode. paired-end options: -ll, --library-length num paired-end library length. in range [1..inf]. default: 220. -le, --library-error num paired-end library length tolerance. in range [0..inf]. default: 50. output format options: -a, --alignment dump the alignment for each match (only razer or fasta format). -pa, --purge-ambiguous purge reads with more than max-hits best matches. -dr, --distance-range num only consider matches with at most num more errors compared to the best. default: output all. -gn, --genome-naming num select how genomes are named (see naming section below). in range [0..1]. default: 0. -rn, --read-naming num select how reads are named (see naming section below). in range [0..3]. default: 0. --full-readid use the whole read id (don't clip after whitespace). -so, --sort-order num select how matches are sorted (see sorting section below). in range [0..1]. default: 0. -pf, --position-format num select begin/end position numbering (see coordinate section below). in range [0..1]. default: 0. -ds, --dont-shrink-alignments disable alignment shrinking in sam. this is required for generating a gold mapping for rabema. filtration options: -fl, --filter str select k-mer filter. one of pigeonhole and swift. default: pigeonhole. -mr, --mutation-rate num set the percent mutation rate (pigeonhole). in range [0..20]. default: 5. -ol, --overlap-length num manually set the overlap length of adjacent k-mers (pigeonhole). in range [0..inf]. -pd, --param-dir dir read user-computed parameter files in the directory dir (swift). -t, --threshold num manually set minimum k-mer count threshold (swift). in range [1..inf]. -tl, --taboo-length num set taboo length (swift). in range [1..inf]. default: 1. -s, --shape bitstring manually set k-mer shape. -oc, --overabundance-cut num set k-mer overabundance cut ratio. in range [0..1]. default: 1. -rl, --repeat-length num skip simple-repeats of length num. in range [1..inf]. default: 1000. -lf, --load-factor num set the load factor for the open addressing k-mer index. in range [1..inf]. default: 1.6. verification options: -mn, --match-n n matches all other characters. default: n matches nothing. -ed, --error-distr file write error distribution to file. -mf, --mismatch-file file write mismatch patterns to file. misc options: -cm, --compact-mult num multiply compaction treshold by this value after reaching and compacting. in range [0..inf]. default: 2.2. -ncf, --no-compact-frac num don't compact if in this last fraction of genome. in range [0..1]. default: 0.05. parallelism options: -pws, --parallel-window-size num collect candidates in windows of this length. in range [1..inf]. default: 500000. -pvs, --parallel-verification-size num verify candidates in packages of this size. in range [1..inf]. default: 100. -pvmpc, --parallel-verification-max-package-count num largest number of packages to create for verification per thread-1. in range [1..inf]. default: 100. -amms, --available-matches-memory-size num bytes of main memory available for storing matches. in range [-1..inf]. default: 0. -mhst, --match-histo-start-threshold num when to start histogram. in range [1..inf]. default: 5. formats, naming, sorting, and coordinate schemes razers 3 supports various output formats. the output format is detected automatically from the file name suffix. .razers razer format .fa, .fasta enhanced fasta format .eland eland format