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

fml-asm 0.1                                       December 2024                                       FML-ASM(1)