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+Bowtie 2 version 2.5.1 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
+Usage: 
+  bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> | --interleaved <i> | -b <bam>} [-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).
+  <i>        Files with interleaved paired-end FASTQ/FASTA reads
+             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
+  <bam>      Files are unaligned BAM sorted by read name.
+  <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)
+  --tab5             query input files are TAB5 .tab5
+  --tab6             query input files are TAB6 .tab6
+  --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
+  -F k:<int>,i:<int> query input files are continuous FASTA where reads
+                     are substrings (k-mers) extracted from a FASTA file <s>
+                     and aligned at offsets 1, 1+i, 1+2i ... end of reference
+  -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)
+  --trim-to [3:|5:]<int> trim reads exceeding <int> bases from either 3' or 5' end
+                     If the read end is not specified then it defaults to 3 (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,1,1.15 (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,1,1.15)
+  --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)
+  --no-1mm-upfront   do not allow 1 mismatch alignments before attempting to
+                     scan for the optimal seeded alignments
+  --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:
+  (default)          look for multiple alignments, report best, with MAPQ
+   OR
+  -k <int>           report up to <int> alns per read; MAPQ not meaningful
+   OR
+  -a/--all           report all alignments; very slow, MAPQ not meaningful
+
+ 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
+  --dovetail         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
+
+ BAM:
+  --align-paired-reads
+                     Bowtie2 will, by default, attempt to align unpaired BAM reads.
+                     Use this option to align paired-end reads instead.
+  --preserve-tags    Preserve tags from the original BAM record by
+                     appending them to the end of the corresponding SAM output.
+
+ 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          suppress SAM records for unaligned reads
+  --no-head          suppress header lines, i.e. lines starting with @
+  --no-sq            suppress @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.
+  --omit-sec-seq     put '*' in SEQ and QUAL fields for secondary alignments.
+  --sam-no-qname-trunc
+                     Suppress standard behavior of truncating readname at first whitespace 
+                     at the expense of generating non-standard SAM.
+  --xeq              Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record.
+  --soft-clipped-unmapped-tlen
+                     Exclude soft-clipped bases when reporting TLEN
+  --sam-append-comment
+                     Append FASTA/FASTQ comment to SAM record
+
+ Performance:
+  -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)
+  --non-deterministic
+                     seed rand. gen. arbitrarily instead of using read attributes
+  --version          print version information and quit
+  -h/--help          print this usage message