Short-read quality control software.

[desmo]

Hi everyone,
I would like to know which are the most useful softwares to control the quality of short reads generated by different kinds of platform.
I've just used FastQC but it's just a visual tool.
Do anyone know similar softwares that make similar analisys, provide some informations about bad reads and filter them?
Thanks

[kga1978]

I have recently started using a combination of cutadapt and prinseq that seems to be working pretty well. Here's an example command that will trim all TruSeq adapters and low quality bases

gunzip *.gz -c | cutadapt -O 6 2> reads.cutadap_log.txt -a AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTG -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTG -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGCCGTCTTCTGCTTG -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTTG -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTTCTGCTTG -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCCGTCTTCTGCTTG -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGCCGTCTTCTGCTTG -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATGCCGTCTTCTGCTTG -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTATCTCGTATGCCGTCTTCTGCTTG -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACATCTCGTATGCCGTCTTCTGCTTG -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCTTCTGCTTG -a CTTCACCGTGCCAGACTAGAGTCAAGCTCAACAGGGTCTTCTTTCCCCGCTG -a GGATGAACGAGATTCCCACTGTCCCTACCTACTATCCAGCGAAACCACAGCC -a CTCCCTTTCGATCGGCCGAGGGCAACGGAGGCCATCGCCCGTCCCTTCGGAA -a CGAGATTCCCACTGTCCCTACCTACTATCCAGCGAAACCACAGCCAAGGGAA -a CCACTCTCGACTGCCGGCGACGGCCGGGTATGGGCCCGACGCTCCAGCGCCA -a TGGAAGTCGGAATCCGCTAAGGAGTGTGTAACAACTCACCTGCCGAATCAAC -a CCTATACCCAGGTCGGACGACCGATTTGCACGTCAGGACCGCTACGGACCTC -a CACGAGCGCACGTGTTAGGACCCGAAAGATGGTGAACTATGCCTGGGCAGGG -a GTCGGAATCCGCTAAGGAGTGTGTAACAACTCACCTGCCGAATCAACTAGCC -a CTCCCGTCCACTCTCGACTGCCGGCGACGGCCGGGTATGGGCCCGACGCTCC -a CGCAGGTTCAGACATTTGGTGTATGTGCTTGGCTGAGGAGCCAATGGGGCGA -a GAACGAGATTCCCACTGTCCCTACCTACTATCCAGCGAAACCACAGCCAAGG -a CAGAAGGGCAAAAGCTCGCTTGATCTTGATTTTCAGTACGAATACAGACCGT -a TTTCGATCGGCCGAGGGCAACGGAGGCCATCGCCCGTCCCTTCGGAACGGCG - | prinseq -fastq stdin -out_good stdout -log reads.prinseq_log.txt -min_len 20 -ns_max_n 4 -min_gc 10 -max_gc 90 -min_qual_mean 18 -trim_qual_left 10 -trim_qual_right 10 | gzip -9 > reads.trimmed.fastq.gz

[simonandrews]

Hi everyone,
I would like to know which are the most useful softwares to control the quality of short reads generated by different kinds of platform.
I've just used FastQC but it's just a visual tool.
Do anyone know similar softwares that make similar analisys, provide some informations about bad reads and filter them?
Thanks

I would be wary about automatically filtering anything which looked odd in a dataset. Some filtering (quality and adapter trimming) is uncontentious and programs like cutadapt seem to do a good enough job for that. Filtering on other measures within your library without actually looking at the data and putting this in the context of the experiment runs the risk of removing interesting biological effects.

We've always said that the tests in FastQC are not intended to tell you whether your data is good or bad, they're there to tell you which aspects of your data you need to consider more closely, or bear in mind when interpreting the results of downstream analysis. We can provide examples of perfectly good sequence data which can fail any of the tests FastQC does.

[desmo]

Thanks. I've not yet decided what strategy is better for my work but yours suggestions were very useful