.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH FML-ASM "1" "January 2023" "fml-asm 0.1" "User Commands"
.SH NAME
fml-asm \- assemble Illumina short reads in small regions
.SH SYNOPSIS
.B fml-asm
[\fI\,options\/\fR] \fI\,<in.fq>\/\fR
.SH OPTIONS
.TP
\fB\-e\fR INT
k\-mer length for error correction (0 for auto; \fB\-1\fR to disable) [0]
.TP
\fB\-c\fR INT1[,INT2]
range of k\-mer & read count thresholds for ec and graph cleaning [4,8]
.TP
\fB\-l\fR INT
min overlap length during initial assembly [33]
.TP
\fB\-r\fR FLOAT
drop an overlap if its length is below maxOvlpLen*FLOAT [0.7]
.TP
\fB\-t\fR INT
number of threads (don't use multi\-threading for small data sets) [1]
.TP
\fB\-d\fR INT
retain a bubble if one side is longer than the other side by >INT\-bp [50]
.TP
\fB\-A\fR
discard heterozygotes (apply this to assemble bacterial genomes; override \fB\-O\fR)
.TP
\fB\-O\fR
don't apply aggressive tip trimming
.TP
\fB\-g\fR
output the assembly graph in the GFA format