ssake(1) [debian man page]
SSAKE(1) General Commands Manual SSAKE(1) NAME
ssake - assembling millions of very short DNA sequences SYNOPSIS
Progressive assembly of millions of short DNA sequences by k-mer search through a prefix tree and 3' extension. OPTIONS
-f Fasta file containing all the [paired (-p 1) / unpaired (-p 0)] reads (required) paired reads must now be separated by ":" -s Fasta file containing sequences to use as seeds exclusively (specify only if different from read set, optional) -m Minimum number of overlapping bases with the seed/contig during overhang consensus build up (default -m 16) -o Minimum number of reads needed to call a base during an extension (default -o 3) -r Minimum base ratio used to accept a overhang consensus base (default -r 0.7) -t Trim up to -t base(s) on the contig end when all possibilities have been exhausted for an extension (default -t 0)> -p Paired-end reads used? (-p 1=yes, -p 0=no, default -p 0) -v Runs in verbose mode (-v 1=yes, -v 0=no, default -v 0, optional) -b Base name for your output files (optional) ============ Options below only considered with -p 1 ============ -d Mean distance expected/observed between paired-end reads (default -d 200, optional) -e Error (%) allowed on mean distance e.g. -e 0.75 == distance +/- 75% (default -e 0.75, optional) -k Minimum number of links (read pairs) to compute scaffold (default -k 2, optional) -a Maximum link ratio between two best contig pairs *higher values lead to least accurate scaffolding* (default -a 0.70, optional) -z Minimum contig size to track paired-end reads (default -z 50, optional) -g Fasta file containing unpaired sequence reads (optional) SEE ALSO
/usr/share/doc/ssake/SSAKE.readme between AUTHORS
This manual page was written by Andreas Tille <tille@debian.org> for the Debian system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any later version published by the Free Software Foundation. On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL. January 2008 SSAKE(1)
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BOWTIE2-ALIGN(1) User Commands BOWTIE2-ALIGN(1) NAME
bowtie2-align - wrapper for bowtie2-align DESCRIPTION
Bowtie 2 version 2.0.0-beta6 by Ben Langmead (blangmea@jhsph.edu) Usage: bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r>} [-S <sam>] <bt2-idx> Index filename prefix (minus trailing .X.bt2). NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible. <m1> Files with #1 mates, paired with files in <m2>. Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). <m2> Files with #2 mates, paired with files in <m1>. Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). <r> Files with unpaired reads. Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). <sam> File for SAM output (default: stdout) <m1>, <m2>, <r> can be comma-separated lists (no whitespace) and can be specified many times. E.g. '-U file1.fq,file2.fq -U file3.fq'. Options (defaults in parentheses): Input: -q query input files are FASTQ .fq/.fastq (default) --qseq query input files are in Illumina's qseq format -f query input files are (multi-)FASTA .fa/.mfa -r query input files are raw one-sequence-per-line -c <m1>, <m2>, <r> are sequences themselves, not files -s/--skip <int> skip the first <int> reads/pairs in the input (none) -u/--upto <int> stop after first <int> reads/pairs (no limit) -5/--trim5 <int> trim <int> bases from 5'/left end of reads (0) -3/--trim3 <int> trim <int> bases from 3'/right end of reads (0) --phred33 qualities are Phred+33 (default) --phred64 qualities are Phred+64 --int-quals qualities encoded as space-delimited integers Presets: Same as: For --end-to-end: --very-fast -D 5 -R 1 -N 0 -L 22 -i S,0,2.50 --fast -D 10 -R 2 -N 0 -L 22 -i S,0,2.50 --sensitive -D 15 -R 2 -N 0 -L 22 -i S,1,1.25 (default) --very-sensitive -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 For --local: --very-fast-local -D 5 -R 1 -N 0 -L 25 -i S,1,2.00 --fast-local -D 10 -R 2 -N 0 -L 22 -i S,1,1.75 --sensitive-local -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default) --very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 Alignment: -N <int> max # mismatches in seed alignment; can be 0 or 1 (0) -L <int> length of seed substrings; must be >3, <32 (22) -i <func> interval between seed substrings w/r/t read len (S,1,1.25) --n-ceil <func> func for max # non-A/C/G/Ts permitted in aln (L,0,0.15) --dpad <int> include <int> extra ref chars on sides of DP table (15) --gbar <int> disallow gaps within <int> nucs of read extremes (4) --ignore-quals treat all quality values as 30 on Phred scale (off) --nofw do not align forward (original) version of read (off) --norc do not align reverse-complement version of read (off) --end-to-end entire read must align; no clipping (on) OR --local local alignment; ends might be soft clipped (off) Scoring: --ma <int> match bonus (0 for --end-to-end, 2 for --local) --mp <int> max penalty for mismatch; lower qual = lower penalty (6) --np <int> penalty for non-A/C/G/Ts in read/ref (1) --rdg <int>,<int> read gap open, extend penalties (5,3) --rfg <int>,<int> reference gap open, extend penalties (5,3) --score-min <func> min acceptable alignment score w/r/t read length (G,20,8 for local, L,-0.6,-0.6 for end-to-end) Reporting: -M <int> look for up to <int>+1 alns; report best, with MAPQ (5 for --end-to-end, 2 for --local) OR -k <int> report up to <int> alns per read; MAPQ not meaningful (off) OR -a/--all report all alignments; very slow (off) Effort: -D <int> give up extending after <int> failed extends in a row (15) -R <int> for reads w/ repetitive seeds, try <int> sets of seeds (2) Paired-end: -I/--minins <int> minimum fragment length (0) -X/--maxins <int> maximum fragment length (500) --fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr) --no-mixed suppress unpaired alignments for paired reads --no-discordant suppress discordant alignments for paired reads --no-dovetail not concordant when mates extend past each other --no-contain not concordant when one mate alignment contains other --no-overlap not concordant when mates overlap at all Output: -t/--time print wall-clock time taken by search phases --un <path> write unpaired reads that didn't align to <path> --al <path> write unpaired reads that aligned at least once to <path> --un-conc <path> write pairs that didn't align concordantly to <path> --al-conc <path> write pairs that aligned concordantly at least once to <path> (Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g. --un-gz <path>, to gzip compress output, or add '-bz2' to bzip2 compress output.) --quiet print nothing to stderr except serious errors --met-file <path> send metrics to file at <path> (off) --met-stderr send metrics to stderr (off) --met <int> report internal counters & metrics every <int> secs (1) --no-unal supppress SAM records for unaligned reads --no-head supppress header lines, i.e. lines starting with @ --no-sq supppress @SQ header lines --rg-id <text> set read group id, reflected in @RG line and RG:Z: opt field --rg <text> add <text> ("lab:value") to @RG line of SAM header. Note: @RG line only printed when --rg-id is set. Performance: -o/--offrate <int> override offrate of index; must be >= index's offrate -p/--threads <int> number of alignment threads to launch (1) --reorder force SAM output order to match order of input reads --mm use memory-mapped I/O for index; many 'bowtie's can share Other: --qc-filter filter out reads that are bad according to QSEQ filter --seed <int> seed for random number generator (0) --version print version information and quit -h/--help print this usage message 64-bit Built on lxcsid Fri Jun 1 20:11:44 UTC 2012 Compiler: gcc version 4.7.0 (Debian 4.7.0-8) Options: -O3 -m64 -msse2 -funroll-loops -g3 Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8} bowtie2-align version 2.0.0-beta6 June 2012 BOWTIE2-ALIGN(1)