fml-asm(1)
assemble Illumina short reads in small regions
Description
FML-ASM
NAME
fml-asm - assemble Illumina short reads in small regions
SYNOPSIS
fml-asm [options] <in.fq>
OPTIONS
-e INT
k-mer length for error correction (0 for auto; -1 to disable) [0]
-c INT1[,INT2]
range of k-mer & read count thresholds for ec and graph cleaning [4,8]
-l INT
min overlap length during initial assembly [33]
-r FLOAT
drop an overlap if its length is below maxOvlpLen*FLOAT [0.7]
-t INT
number of threads (don’t use multi-threading for small data sets) [1]
-d INT
retain a bubble if one side is longer than the other side by >INT-bp [50]
|
-A |
discard heterozygotes (apply this to assemble bacterial genomes; override -O) | ||
|
-O |
don’t apply aggressive tip trimming | ||
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-g |
output the assembly graph in the GFA format |