HTSeqQC - 1.0

This App runs HTSeqQC (version 1.0) to:

  • HTSeqQC is an automated quality control analysis tool for a single and paired-end high-throughput sequencing data (HTS) generated from Illumina sequencing platforms.

Tool Creator

Renesh Bedre

Quick Start

Test Data

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

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.

Input file(s)

Input file(s) 1-  Single end input files or left files for paired-end data (.fastq, .fq). 

Input file(s) 2- Right files for paired-end data


QUAL_FMT- Quality value format [1= Illumina 1.8, 2= Illumina 1.3,3= Sanger]. If quality format not provided, it will automatically detect based on sequence data

N_CONT- Filter the reads containing given % of uncalled bases(N)

ADPT_SEQS- Trim the adapter and truncate the read sequence

MIN_SIZE- Filter the reads which are lesser than minimum size

ADPT_MATCH- Truncate the read sequence if it matches to adapter sequence equal or more than given percent (0.0-1.0) [default=0.9]

QUAL_THRESH- Filter the read sequence if average quality of bases in reads is lower than threshold (1-40) [default:20]

TRIM_OPT- If trim option set to True, the reads with low quality (as defined by option --qthr) will be trimmed instead of discarding [True|False] [default: False]

WIND_SIZE- The window size for trimming (5->3) the reads. This option should always set when -trim option is defined [default: 5]

MIN_LEN_FILT- Minimum length of the reads to retain after trimming

Output File(s)

HTSeqQC produces the filtered cleaned HTS data as FASTQ/FASTA files, and statistics and visualization of filtered cleaned HTS datasets. 

OUT_FMT- Output file format (fastq/fasta) [default:fastq]

VIS_OPT- No figures will be produced [True|False]

Tool Source for App