NGS-eval


		NGS-eval: NGS Error analysis and VAriant detection tooL

The recent major upgrade on our compute server, has lead to some configuration issues that turn out to be very hard to resolve.

We are still working on this, and hope to have the server back online in the course of this month (June).

We apologise again for the inconvenience,

and thank you for your continued patience.

In amplicon-based NGS sequencing runs, often a mixture of known bacteria, a so-called mock, is included as one of the samples. This sample can be used to tune processing pipelines and to calculate error rates. The latter assumes that we know the exact marker gene sequence. However, even the same bacterial strain can show variants with respect to its database sequence. Indeed, amplicons can also be used to confirm species and to uncover new sequence variants.
NGS-eval is a web server tailored to calculate sequencing error rates as well as to detect new variants. This server can also be used to correct the mock reference sequences. You upload your (trimmed) reference sequences and the (processed) reads of your mock sample. This typically contains a few thousand reads, which are processed in several minutes. The output supports interactive plotting of the errors for each reference sequence.
Documentation:

Introduction to the NGS-eval server.

The example output shows the results of a mock sample, where 16S rDNA (V4) amplicon reads have been mapped to the 17 16S rDNA reference sequences of bacteria in the sample. This example contains 43707 (chimera-filtered) forward reads from a MiSeq 250-nt paired-end run (FASTQ format, gzipped size: 4.7Mb). You can to reproduce this output.

References:
May, A., Abeln, S., Buijs, M.J., Heringa, J., Crielaard, W. and Brandt, B.W. (2015). NGS-eval: NGS Error analysis and novel sequence VAriant detection tooL. Nucleic Acids Research 43:W301-W305.

May, A., Abeln, S., Crielaard, W., Heringa, J. and Brandt, B.W. (2014) Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations. Bioinformatics 30(11):1530-1538.

Sequence Input

Reference FASTA file:

NGS reads file:

NGS qual file:

Reverse reads:

Format: detect FASTA FASTQ

Compression: detect uncompressed gzip zip

Options

Forward primer:

Reverse primer:

Truncation length:

Set truncation length to longest read

Expand degenerate bases

PCR reference sequences

Remove primers from the reference amplicon sequences

Advanced Options (optional):

Read mapping Identity: %

Needle gap penalties Gap open:

Gap extend:

E-mail address (optional):

The NGS-eval server was developed by Bernd Brandt.

NGS-eval: NGS Error analysis and VAriant detection tooL