# Miniasm 0.3


## Miniasm

Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It
takes all-vs-all read self-mappings (typically by minimap) 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.

Location and version:

```console
$ which miniasm
/local/cluster/bin/miniasm
$ miniasm -V
0.3-r179
```

help message:

```console
$ miniasm --help
miniasm: invalid option -- '-'
Usage: miniasm [options] <in.paf>
Options:
  Pre-selection:
    -R          prefilter clearly contained reads (2-pass required)
    -m INT      min match length [100]
    -i FLOAT    min identity [0.05]
    -s INT      min span [2000]
    -c INT      min coverage [3]
  Overlap:
    -o INT      min overlap [same as -s]
    -h INT      max over hang length [0]
    -I FLOAT    min end-to-end match ratio [0.8]
  Layout:
    -g INT      max gap differences between reads for trans-reduction [1000]
    -d INT      max distance for bubble popping [50000]
    -e INT      small unitig threshold [4]
    -f FILE     read sequences []
    -n INT      rounds of short overlap removal [3]
    -r FLOAT[,FLOAT]
                max and min overlap drop ratio [0.7,0.5]
    -F FLOAT    aggressive overlap drop ratio in the end [0.8]
  Miscellaneous:
    -p STR      output information: bed, paf, sg or ug [ug]
    -b          both directions of an arc are present in input
    -1          skip 1-pass read selection
    -2          skip 2-pass read selection
    -V          print version number

See miniasm.1 for detailed description of the command-line options.
```

software ref: <https://github.com/lh3/miniasm>  
research ref: NA