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FML-ASM(1) User Commands FML-ASM(1)

NAME

fml-asm - assemble Illumina short reads in small regions

SYNOPSIS

fml-asm [options] <in.fq>

OPTIONS

k-mer length for error correction (0 for auto; -1 to disable) [0]
range of k-mer & read count thresholds for ec and graph cleaning [4,8]
min overlap length during initial assembly [33]
drop an overlap if its length is below maxOvlpLen*FLOAT [0.7]
number of threads (don't use multi-threading for small data sets) [1]
retain a bubble if one side is longer than the other side by >INT-bp [50]
discard heterozygotes (apply this to assemble bacterial genomes; override -O)
don't apply aggressive tip trimming
output the assembly graph in the GFA format
January 2023 fml-asm 0.1