---
name: "miniasm"
section: "1"
platform: "linux"
package: "miniasm"
version: "0.3+dfsg-4"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/miniasm"
---

# miniasm(1)

de novo assembler for long read sequences

## 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 **-Rc***2* 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)](/minimap/1.md) 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)](/minimap/1.md)