fml-asm - assemble Illumina short reads in small regions
fml-asm [options] <in.fq>
- -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