SYNOPSIS
miniasm [-b12V] [-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
- -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 controled 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:
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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:
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