The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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Nanofilt - 2.5.0

This App runs nanofilt (version 2.5.0) to:

  • Filtering on quality and/or read length, and other trimming options with different user provided filters.

App Creator

Reetu Tuteja

Quick Start

  • Nanofilt 2.5.0 takes one fastq file as input. 

Test Data

Icon

Test data for this is available in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> nanoqc 0.9.1

Input File(s)

Use the LomanLabz_PC_Ecoli_K12_R7.3_2549_1_ch8_file30_strand.fq for an example run. 

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file to get the output provided in the section below.

 

NanoFilt [-h] [-v] [--logfile LOGFILE] [-l LENGTH]
                [--maxlength MAXLENGTH] [-q QUALITY] [--minGC MINGC]
                [--maxGC MAXGC] [--headcrop HEADCROP] [--tailcrop TAILCROP]
                [-s SUMMARY] [--readtype {1D,2D,1D2}]
                [input]

Perform quality and/or length and/or GC filtering of (long read) fastq data. Reads on stdin.

General options:
  -h, --help            show the help and exit
  -v, --version         Print version and exit.
  --logfile LOGFILE     Specify the path and filename for the log file.
  input                 input, uncompressed fastq file (optional)

Options for filtering reads on.:
  -l, --length LENGTH   Filter on a minimum read length
  --maxlength MAXLENGTH Filter on a maximum read length
  -q, --quality QUALITY Filter on a minimum average read quality score
  --minGC MINGC         Sequences must have GC content >= to this. Float between 0.0 and 1.0. Ignored if
                        using summary file.
  --maxGC MAXGC         Sequences must have GC content <= to this. Float between 0.0 and 1.0. Ignored if
                        using summary file.

Options for trimming reads.:
  --headcrop HEADCROP   Trim n nucleotides from start of read
  --tailcrop TAILCROP   Trim n nucleotides from end of read

Input options.: uncompressed fastq files.
  -s, --summary SUMMARY Use albacore or guppy summary file for quality scores
  --readtype            Which read type to extract information about from summary. Options are 1D, 2D or 1D2

Output File(s)

Output file- highquality-reads.fq

Tool Source for App

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