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