Provided by: miniasm_0.3+dfsg-1_amd64 
NAME
miniasm - de novo assembler for long read sequences
SYNOPSIS
miniasm [-b12VR] [-m minMatch] [-i minIden] [-s minSpan] [-c minCov] [-o minOvlp] [-h maxHang] [-I
intThres] [-g maxGapDiff] [-d maxBubDist] [-e minUtgSize] [-f readFile] [-n nRounds] [-r dropRatio] [-F
finalDropRatio] [-p outputInfo] mapping.paf > output.gfa
DESCRIPTION
Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-
mappings in the PAF format as input and outputs an assembly graph in the GFA format. Different from
mainstream assemblers, miniasm does not have a consensus step. It simply concatenates pieces of read
sequences to generate the final unitig sequences. Thus the per-base error rate is similar to the raw
input reads.
OPTIONS
Preselection options
-R Pre-filter clearly contained short reads. In this mode, mapping.paf is read twice. The first
pass identifies contained reads without loading hits to RAM; the second pass skips contained
reads and load the rest into RAM. Due to the 2-pass behavior, the peak RAM is greatly reduced,
but mapping.paf has to be a normal file, not a stream. When this option is in use, it is
recommended to reduce -c to 2, as there are fewer reads after pre-filtering. Applying -Rc2
sometimes improves assembly.
-m INT Drop mappings having less than INT matching bases (col10 in PAF) [100]. This option has the
same role as -L of minimap.
-s INT Drop mappings shorter than INT-bp [1000]. This option also affects the second round of read
filtering and minimal overlap length.
-i FLOAT During read filtering, ignore mappings with col10/col11 below FLOAT [0.05]. Ignored mappings
are still used for read overlaps.
-c INT Minimal coverage by other reads [3]. In the first round of filtering, miniasm finds the longest
region covered by INT or more reads. In the second round, it in addition requires each
remaining base to be covered by INT bases at least minSpan/2 from the ends of other reads.
Overlapping options
-o INT Minimal overlap length [same as minSpan]
-h INT Maximum overhang length [1000]. An overhang is an unmapped region that should be mapped given a
true overlap or true containment. If the overhang is too long, the mapping is considered an
internal match and will be ignored.
-I FLOAT Minimal ratio of mapping length to mapping+overhang length for a mapping considered a
containment or an overlap [0.8]. This option has a similar role to -h, except that it controls
the ratio, not length.
Graph layout options
-g INT Maximal gap differences between two reads in a mapping [1000]. This parameter is only used for
transitive reduction.
-d INT Maximal probing distance for bubble popping [50000]. Bubbles longer than INT will not be
popped.
-e INT A unitig is considered small if it is composed of less than INT reads [4]. Miniasm may try to
remove small unitigs at various steps.
-f FILE Read sequence file in FASTA or FASTQ format for generating unitig sequences [null]. If this
option is absent, miniasm produces a GFA output without sequences.
-r FLOAT1,[FLOAT2]
Max and min overlap drop ratio [0.7,0.5]. Let overlap(v->w) be the overlap length of edge v->w
and maxovlp(v)=max_w{overlap(v->w)} be the length of largest overlap. Miniasm drops overlap
v->w if overlap(v->w)/maxovlp(v) is below a threshold controlled by this option. Miniasm
applies nRounds rounds of short overlap removal with an increasing threshold between FLOAT1 and
FLOAT2.
-n INT Rounds of short overlap removal [3].
-F FLOAT Overlap drop ratio threshold after short unitig removal [0.8]
Miscellaneous options
-b Indicate that in the input, the same mapping is likely to be given twice
-1 Skip the first round of pre-assembly read selection
-2 Skip the second round of pre-assembly read selection
-p STR Output information and format [ug]. Possible STR values include - bed: post-filtered read
regions in the BED format; paf: mappings between post-filtered reads; sg: read overlap graph in
the GFA format; ug: unitig graph in the GFA format.
-V Print version number to stdout
INPUT FORMAT
Miniasm reads mapping positions in the Pairwise mApping Format (PAF), which 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) │
└────┴────────┴─────────────────────────────────────────────────────────────┘
Please see minimap(1) for the detailed description of each field.
OUTPUT FORMAT
Miniasm outputs the assembly in the Graphical Fragment Assembly format (GFA). It is a line based TAB-
delimited format, with the leading letter indicates the type of the line. The following table gives the
line types used by miniasm:
┌─────┬─────────────┬──────────────────────────────────────────────────────┐
│Line │ Comment │ Fixed fields │
├─────┼─────────────┼──────────────────────────────────────────────────────┤
│ H │ Header │ N/A │
│ S │ Segment │ segName segSeq │
│ L │ Overlap │ segName1 segOri1 segName2 segOri2 ovlpCIGAR │
│ a │ Golden path │ utgName utgStart readName:rStart-rEnd readOri incLen │
└─────┴─────────────┴──────────────────────────────────────────────────────┘
An `a' line indicates that the unitig subsequence in [utgStart,utgStart+incLen) is taken from read
readName in region [rStart-1,rStart-1+incLen). It is not a standard GFA line. An `x' line gives a brief
summary of each unitig, which can be inferred from `S' and `a' lines.
SEE ALSO
minimap(1)