Calling nvBowtie_usage() prints available arguments that can be passed to the nvBowtie() function.
Value
An invisible Integer of call status. The value is 0 when there is not any mistakes Otherwise the value is non-zero.
References
Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature methods, 9(4), 357-359.
Examples
nvBowtie_usage()
#> [1] "options:"
#> [1] "General:"
#> [1] " --verbosity int [5] verbosity level"
#> [1] " --upto | -u int [-1] maximum number of reads to process"
#> [1] " --trim3 | -3 int [0] trim the first N bases of 3'"
#> [1] " --trim5 | -5 int [0] trim the first N bases of 5'"
#> [1] " --nofw [false] do not align the forward strand"
#> [1] " --norc [false] do not align the reverse-complemented strand"
#> [1] " --device int [0] select the given cuda device(s) (e.g. --device 0 --device 1 ...)"
#> [1] " --file-ref [false] load reference from file"
#> [1] " --server-ref [false] load reference from server"
#> [1] " --phred33 [true] qualities are ASCII characters equal to Phred quality + 33"
#> [1] " --phred64 [false] qualities are ASCII characters equal to Phred quality + 64"
#> [1] " --solexa-quals [false] qualities are in the Solexa format"
#> [1] " --rg-id string add the RG-ID field of the SAM output header"
#> [1] " --rg string,val add an RG-TAG field of the SAM output header"
#> [1] " --cache-writes bool [false] speed up writes on disk"
#> [1] "Paired-End:"
#> [1] " --ff [false] paired mates are forward-forward"
#> [1] " --fr [true] paired mates are forward-reverse"
#> [1] " --rf [false] paired mates are reverse-forwardd"
#> [1] " --rr [false] paired mates are reverse-reverse"
#> [1] " --minins | -I int [0] minimum insert length"
#> [1] " --maxins | -X int [500] maximum insert length"
#> [1] " --overlap [true] allow overlapping mates"
#> [1] " --no-mixed [false] only report paired alignments"
#> [1] " --ungapped-mates | -ug perform ungapped mate alignment"
#> [1] "Seeding:"
#> [1] " --seed-len | -L int [22] seed lengths"
#> [1] " --seed-freq | -i {G|L|S},x,y seed interval, as x + y*func(read-len) (G=log,L=linear,S=sqrt)"
#> [1] " --max-hits int [100] maximum amount of seed hits"
#> [1] " --max-reseed | -R int [2] number of reseeding rounds"
#> [1] " --top bool [false] explore top seed entirely"
#> [1] " --N bool [false] allow substitution in seed"
#> [1] "Extension:"
#> [1] " --mode {best,best-exact,all} [best] alignment mode\n"
#> [1] " --all | -a [false] perform all-mapping (i.e. find and report all alignments)"
#> [1] " --local [false] perform local alignment"
#> [1] " --rand [true] randomized seed hit selection"
#> [1] " --no-rand [false] do not randomize seed hit selection"
#> [1] " --max-dist int [15] maximum edit distance"
#> [1] " --max-effort-init int [15] initial maximum number of consecutive extension failures"
#> [1] " --max-effort | -D int [15] maximum number of consecutive extension failures"
#> [1] " --min-ext int [30] minimum number of extensions per read"
#> [1] " --max-ext int [400] maximum number of extensions per read"
#> [1] " --very-fast apply the very-fast presets"
#> [1] " --fast apply the fast presets"
#> [1] " --sensitive apply the sensitive presets"
#> [1] " --very-sensitive apply the very-sensitive presets"
#> [1] " --very-fast-local apply the very-fast presets"
#> [1] " --fast-local apply the fast presets"
#> [1] " --sensitive-local apply the sensitive presets"
#> [1] " --very-sensitive-local apply the very-sensitive presets"
#> [1] "Scoring:"
#> [1] " --scoring {sw|ed|wfa} [ed] Smith-Waterman / Edit-Distance / Wfa scoring"
#> [1] " --score-min {G|L|S},x,y minimum score function, as x + y*func(read-len)"
#> [1] " --ma int match bonus"
#> [1] " --mp int,int mismatch min/max penalties"
#> [1] " --np int N penalty"
#> [1] " --rdg int,int read open/extension gap penalties"
#> [1] " --rfg int,int reference open/extension gap penalties"
#> [1] "Alternative:"
#> [1] " --wfa Activate wavefront algorithm"
#> [1] "Reporting:"
#> [1] " --mapQ-filter | -Q int [0] minimum mapQ threshold"
#> [1] ""
#> [1] ""
#> [1] "Default values are indicated in brackets []."
#> [1] ""
#> [1] "The '--scoring-scheme filename' option allows to provide a custom Smith-Waterman scoring"
#> [1] "scheme through a text file, where each line must contain a token value pair."
#> [1] " The tokens and default values are reported below:"
#> [1] "* match 0 // local alignment: 2"
#> [1] "* mm-penalty-min 2"
#> [1] "* mm-penalty-max 6"
#> [1] "* N-penalty-min 1"
#> [1] "* N-penalty-max 1"
#> [1] "* score-min-const -0.6 // local alignment: 0"
#> [1] "* score-min-coeff -0.6 // local alignment: 10"
#> [1] "* score-min-type linear // local alignment: log"
#> [1] "* N-ceil-const 0"
#> [1] "* N-ceil-coeff 0.15"
#> [1] "* read-gap-const 5"
#> [1] "* read-gap-coeff 3"
#> [1] "* ref-gap-const 5"
#> [1] "* ref-gap-coeff 3"
#> [1] "* gap-free 5"