IlluQC Parallel (from NGS QC Toolkit)

Tool for quality control of sequencing data generated using Illumina platform (uses multiple CPUs).

Paired ends read:

True - Paired-end read files (FASTQ)

False - Reverse-end read files (FASTQ)

Input files:

Forwards Reads File (FASTQ)

Reverse Reads File (FASTQ)

Primer/Adaptor Libraries

1 = Genomic DNA/Chip-seq Library

2 = Paired End DNA Library

3 = DpnII gene expression Library

4 = NlaIII gene expression Library

5 = Small RNA Library

6 = Multiplexing DNA Library

N = DO NOT FILTER for Primer/Adaptor

F = Use custome file. (Choose input on next dialog)

Primer/Adaptor File

Use this only if 'F' is chosen in the Primer/Adaptor Libraries dialog.

FASTQ Variants:

Sanger (Phred+33, 33 to 73)

Solexa (Phred+64, 59 to 104)

Illumina (1.3+) (Phred+64, 64 to 104)

Illumina (1.5+) (Phred+64, 66 to 104)

Illumina (1.8+) (Phred+33, 33 to 74)

Automatic detection of FASTQ variant

Input format:

1. Forwards Read File (FASTQ)
2. Reverse Read File (FASTQ)

Output format:

1. Forwards filtered file (FASTQ)
2. Reverse filtered file (FASTQ)
3. Forwards+Reverse Unpared HQ Reads file (FASTQ)

http://59.163.192.90:8080/ngsqctoolkit/

http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030619

Patel RK, Jain M (2012). NGS QC Toolkit: A toolkit for quality control of next generation sequencing data. PLoS ONE, 7(2): e30619 .