miniasm.1

.TH miniasm 1 "24 January 2016" "miniasm-0.2+dirty" "Bioinformatics tools"

.SH NAME
.PP
miniasm - de novo assembler for long read sequences

.SH SYNOPSIS
.PP
miniasm
.RB [ -b12VR ]
.RB [ -m
.IR minMatch ]
.RB [ -i
.IR minIden ]
.RB [ -s
.IR minSpan ]
.RB [ -c
.IR minCov ]
.RB [ -o
.IR minOvlp ]
.RB [ -h
.IR maxHang ]
.RB [ -I
.IR intThres ]
.RB [ -g
.IR maxGapDiff ]
.RB [ -d
.IR maxBubDist ]
.RB [ -e
.IR minUtgSize ]
.RB [ -f
.IR readFile ]
.RB [ -n
.IR nRounds ]
.RB [ -r
.IR dropRatio ]
.RB [ -F
.IR finalDropRatio ]
.RB [ -p
.IR outputInfo ]
.I mapping.paf
>
.I output.gfa

.SH DESCRIPTION
.PP
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.

.SH OPTIONS

.SS Preselection options

.TP 10
.BI -R
Pre-filter clearly contained short reads. In this mode,
.I 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
.I mapping.paf
has to be a normal file, not a stream. When this option is in use, it is
recommended to reduce
.B -c
to 2, as there are fewer reads after pre-filtering. Applying
.BI -Rc 2
sometimes improves assembly.

.TP
.BI -m \ INT
Drop mappings having less than
.I INT
matching bases (col10 in PAF) [100]. This option has the same role as
.B -L
of minimap.

.TP
.BI -s \ INT
Drop mappings shorter than
.IR INT -bp
[1000]. This option also affects the second round of read filtering and minimal
overlap length.

.TP
.BI -i \ FLOAT
During read filtering, ignore mappings with col10/col11 below
.I FLOAT
[0.05]. Ignored mappings are still used for read overlaps.

.TP
.BI -c \ INT
Minimal coverage by other reads [3]. In the first round of filtering, miniasm
finds the longest region covered by
.I INT
or more reads. In the second round, it in addition requires each remaining base
to be covered by
.I INT
bases at least
.IR minSpan /2
from the ends of other reads.

.SS Overlapping options

.TP 10
.BI -o \ INT
Minimal overlap length [same as
.IR minSpan ]

.TP
.BI -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.

.TP
.BI -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
.BR -h ,
except that it controls the ratio, not length.

.SS Graph layout options

.TP 10
.BI -g \ INT
Maximal gap differences between two reads in a mapping [1000]. This parameter
is only used for transitive reduction.

.TP
.BI -d \ INT
Maximal probing distance for bubble popping [50000]. Bubbles longer than
.I INT
will not be popped.

.TP
.BI -e \ INT
A unitig is considered small if it is composed of less than 
.I INT
reads [4]. Miniasm may try to remove small unitigs at various steps.

.TP
.BI -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.

.TP
.BI -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
.I nRounds
rounds of short overlap removal with an increasing threshold between
.I FLOAT1
and
.IR FLOAT2 .

.TP
.BI -n \ INT
Rounds of short overlap removal [3].

.TP
.BI -F \ FLOAT
Overlap drop ratio threshold after short unitig removal [0.8]

.SS Miscellaneous options

.TP 10
.B -b
Indicate that in the input, the same mapping is likely to be given twice

.TP
.B -1
Skip the first round of pre-assembly read selection

.TP
.B -2
Skip the second round of pre-assembly read selection

.TP
.BI -p \ STR
Output information and format [ug]. Possible
.I STR
values include -
.BR bed :
post-filtered read regions in the BED format;
.BR paf :
mappings between post-filtered reads;
.BR sg :
read overlap graph in the GFA format;
.BR ug :
unitig graph in the GFA format.

.TP
.B -V
Print version number to stdout

.SH INPUT FORMAT

.PP
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:

.TS
center box;
cb | cb | cb
r | c | l .
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)
.TE

.PP
Please see minimap(1) for the detailed description of each field.

.SH OUTPUT FORMAT

.PP
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:

.TS
center box;
cb | cb | cb
c | l | l .
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
.TE

.PP
An `a' line indicates that the unitig subsequence in
.RI [ utgStart , utgStart + incLen )
is taken from read
.I readName
in region
.RI [ 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.

.SH SEE ALSO
.PP
minimap(1)