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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.
.TH FILTLONG "1" "January 2019" "filtlong 0.2.0" "User Commands"
.SH NAME
filtlong \- quality filtering tool for Nanopore and PacBio reads
.SH SYNOPSIS
.B filtlong
{OPTIONS} [input_reads]
.SH OPTIONS
.SS "positional arguments:"
.TP
input_reads
input long reads to be filtered
.SS "optional arguments:"
.IP
output thresholds:
.TP
\fB\-t[int]\fR, \fB\-\-target_bases\fR [int]
keep only the best reads up to this many total bases
.TP
\fB\-p[float]\fR, \fB\-\-keep_percent\fR [float]
keep only this percentage of the best reads (measured by bases)
.TP
\fB\-\-min_length\fR [int]
minimum length threshold
.TP
\fB\-\-min_mean_q\fR [float]
minimum mean quality threshold
.TP
\fB\-\-min_window_q\fR [float]
minimum window quality threshold
.IP
external references (if provided, read quality will be determined using these instead of from the Phred scores):
.TP
\fB\-a[file]\fR, \fB\-\-assembly\fR [file]
reference assembly in FASTA format
.TP
\fB\-1[file]\fR, \fB\-\-illumina_1\fR [file]
reference Illumina reads in FASTQ format
.TP
\fB\-2[file]\fR, \fB\-\-illumina_2\fR [file]
reference Illumina reads in FASTQ format
.IP
score weights (control the relative contribution of each score to the final read score):
.TP
\fB\-\-length_weight\fR [float]
weight given to the length score (default: 1)
.TP
\fB\-\-mean_q_weight\fR [float]
weight given to the mean quality score (default: 1)
.TP
\fB\-\-window_q_weight\fR [float]
weight given to the window quality score (default: 1)
.IP
read manipulation:
.TP
\fB\-\-trim\fR
trim non\-k\-mer\-matching bases from start/end of reads
.TP
\fB\-\-split\fR [split]
split reads at this many (or more) consecutive non\-k\-mer\-matching bases
.IP
other:
.TP
\fB\-\-window_size\fR [int]
size of sliding window used when measuring window quality (default: 250)
.TP
\fB\-\-verbose\fR
verbose output to stderr with info for each read
.TP
\fB\-\-version\fR
display the program version and quit
.TP
\fB\-h\fR, \fB\-\-help\fR
display this help menu
.PP
For
more
information,
go
to:
https://github.com/rrwick/Filtlong
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
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