kbm2 - simple instance which implemented kmer-binmap
kbm <options> [start|list|stop]
Program: kbm is a simple instance which implemented
kmer-binmap
- it maps query sequence against reference by kmer matching matched
kmer-pairs are bined (256bp) and counted in a matrix dynamic programming
is used to search the best path
Version: 2.5 (20190621) Author: Jue Ruan
<ruanjue@gmail.com>
-i <string> File(s) of query sequences, +,
[STDIN]
-d <string> File(s) of reference sequences, +,
[<-i>]
- -L <int>
- Choose the longest subread and drop reads shorter than <int> (5000
recommended for PacBio) [0] Negative integer indicate keeping read names,
e.g. -5000.
-o <string> Output file, [STDOUT]
- -I
- Interactive mode e.g. `mkfifo pipe` then `while true; do cat pipe
&& sleep 1; done | kbm -t 8 -I -d ref.fa
-i - -Hk 21 -S 4` then `cat 1.fq >pipe; cat 2.fq
>pipe`, fastq format is better in interaction
- -f
- Force overwrite
- -t <int>
- Number of threads, 0: all cores, [1]
- -k <int>
- Kmer-f size, <= 23, [0]
- -p <int>
- Kmer-p size, <= 23, [21]
- -K <float>
- Filter high frequency kmers, maybe repetitive, [1000] if K >= 1, take
the integer value as cutoff, MUST <= 65535 else, mask the top fraction
part high frequency kmers
- -E <int>
- Min kmer frequency, [1]
- -O <int>
- Filter low complexity bins (#indexed_kmer less than <-O>), [2]
- -S <float>
- Subsampling kmers, 1/(<-S>) kmers are indexed, [4.00] -S is
very useful in saving memory and speeding up please note that subsampling
kmers will have less matched length
- -B <int>
- Select no more than n seeds in a query bin, [256] If you are using shared
kbmidx by other process using -D too, it will bring wrong
behavior
- -D <int>
- Strand of alignment, 1: forward, 2: reverse, 3: both, [3]
- -X <int>
- Max number of bin(256bp) in one gap, [4]
- -Y <int>
- Max number of bin(256bp) in one deviation, [4]
- -Z <float>
- Max fraction of gapped BINs / aligned BINs, [0.6]
- -x <int>
- penalty for BIN gap, [-7]
- -y <int>
- penalty for BIN deviation, [-21]
- -z <int>
- Enable refine alignment with -p <-z> [0]
- -l <int>
- Min alignment length, [2048]
- -m <int>
- Min matched length, [200]
- -s <float>
- Min similarity, calculated by kmer matched length / aligned length,
[0.05]
- -r <float>
- Max length variation of two aligned fragments, [0.25]
- -c
- Insist to query contained reads against all
- -C
- Chainning alignments
- -n <int>
- Max hits per query, [1000]
- -T <int>
- For debug, [0]
-W <string> Dump kbm index to file, [NULL]
-R <string> Load kbm index from file, [NULL]
- -q
- Quiet
- -V
- Print version information and then exit
Server start: {kbm -R <wt.fa.kbmidx> start}, will
mmap wt.fa.kbmidx into mmeory Server list: {kbm -R
<wt.fa.kbmidx> list [10]}, will list the object tree in file Server
stop: {kbm -R <wt.fa.kbmidx> stop}, will remove the mmap
object
This manpage was written by Andreas Tille for the Debian
distribution and
can be used for any other usage of the program.