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:
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$ which miniasm
/local/cluster/bin/miniasm
$ miniasm -V
0.3-r179
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help message:
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$ 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.
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software ref: https://github.com/lh3/miniasm
research ref: NA