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

-g

output the assembly graph in the GFA format