kbm21

Usage

Overview

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 <[email protected]>

Options

-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