Provided by: minimap_0.2-3_amd64 
NAME
minimap - fast mapping between long DNA sequences
SYNOPSIS
minimap [-lSOV] [-k kmer] [-w winSize] [-I batchSize] [-d dumpFile] [-f occThres] [-r bandWidth] [-m
minShared] [-c minCount] [-L minMatch] [-g maxGap] [-T dustThres] [-t nThreads] [-x preset] target.fa
query.fa > output.paf
DESCRIPTION
Minimap is a tool to efficiently find multiple approximate mapping positions between two sets of long
sequences, such as between reads and reference genomes, between genomes and between long noisy reads.
Minimap has an indexing and a mapping phase. In the indexing phase, it collects all minimizers of a large
batch of target sequences in a hash table; in the mapping phase, it identifies good clusters of colinear
minimizer hits. Minimap does not generate detailed alignments between the target and the query sequences.
It only outputs the approximate start and the end coordinates of these clusters.
OPTIONS
Indexing options
-k INT Minimizer k-mer length [15]
-w INT Minimizer window size [2/3 of k-mer length]. A minimizer is the smallest k-mer in a window of w
consecutive k-mers.
-I NUM Load at most NUM target bases into RAM for indexing [4G]. If there are more than NUM bases in
target.fa, minimap needs to read query.fa multiple times to map it against each batch of target
sequences. NUM may be ending with k/K/m/M/g/G.
-d FILE Dump minimizer index to FILE [no dump]
-l Indicate that target.fa is in fact a minimizer index generated by option -d, not a FASTA or
FASTQ file.
Mapping options
-f FLOAT Ignore top FLOAT fraction of most occurring minimizers [0.001]
-r INT Approximate bandwidth for initial minimizer hits clustering [500]. A minimizer hit is a
minimizer present in both the target and query sequences. A minimizer hit cluster is a group of
potentially colinear minimizer hits between a target and a query sequence.
-m FLOAT Merge initial minimizer hit clusters if FLOAT or higher fraction of minimizers are shared
between the clusters [0.5]
-c INT Retain a minimizer hit cluster if it contains INT or more minimizer hits [4]
-L INT Discard a minimizer hit cluster if after colinearization, the number of matching bases is below
INT [40]. This option mainly reduces the size of output. It has little effect on the speed and
peak memory.
-g INT Split a minimizer hit cluster at a gap INT-bp or longer that does not contain any minimizer
hits [10000]
-T INT Mask regions on query sequences with SDUST score threshold INT; 0 to disable [0]. SDUST is an
algorithm to identify low-complexity subsequences. It is not enabled by default. If SDUST is
preferred, a value between 20 and 25 is recommended. A higher threshold masks less sequences.
-S Perform all-vs-all mapping. In this mode, if the query sequence name is lexicographically
larger than the target sequence name, the hits between them will be suppressed; if the query
sequence name is the same as the target name, diagonal minimizer hits will also be suppressed.
-O Drop a minimizer hit if it is far away from other hits (EXPERIMENTAL). This option is useful
for mapping long chromosomes from two diverged species.
-x STR Changing multiple settings based on STR [not set]. It is recommended to apply this option
before other options, such that the following options may override the multiple settings
modified by this option.
ava10k for PacBio or Oxford Nanopore all-vs-all read mapping (-Sw5 -L100 -m0).
Input/output options
-t INT Number of threads [3]. Minimap uses at most three threads when collecting minimizers on target
sequences, and uses up to INT+1 threads when mapping (the extra thread is for I/O, which is
frequently idle and takes little CPU time).
-V Print version number to stdout
OUTPUT FORMAT
Minimap outputs mapping positions in the Pairwise mApping Format (PAF). PAF is a TAB-delimited text
format with each line consisting of at least 12 fields as are described in the following table:
┌────┬────────┬─────────────────────────────────────────────────────────────┐
│Col │ Type │ Description │
├────┼────────┼─────────────────────────────────────────────────────────────┤
│ 1 │ string │ Query sequence name │
│ 2 │ int │ Query sequence length │
│ 3 │ int │ Query start coordinate (0-based) │
│ 4 │ int │ Query end coordinate (0-based) │
│ 5 │ char │ `+' if query and target on the same strand; `-' if opposite │
│ 6 │ string │ Target sequence name │
│ 7 │ int │ Target sequence length │
│ 8 │ int │ Target start coordinate on the original strand │
│ 9 │ int │ Target end coordinate on the original strand │
│ 10 │ int │ Number of matching bases in the mapping │
│ 11 │ int │ Number bases, including gaps, in the mapping │
│ 12 │ int │ Mapping quality (0-255 with 255 for missing) │
└────┴────────┴─────────────────────────────────────────────────────────────┘
When the alignment is available, column 11 gives the total number of sequence matches, mismatches and
gaps in the alignment; column 10 divided by column 11 gives the alignment identity. As minimap does not
generate detailed alignment, these two columns are approximate. PAF may optionally have additional fields
in the SAM-like typed key-value format. Minimap writes the number of minimizer hits in a cluster to the
cm tag.
SEE ALSO
miniasm(1)