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Introduction Version

Q2FeatureInferenceSE

TASK
Typing name :  TASK.gws_ubiome.Qiime2FeatureTableExtractorSE Brick :  gws_ubiome v

Inference of ASVs from single-end sequencing

Qiime2FeatureTableExtractorSE class.

This task infers Amplicon Sequence Variants (ASVs) using the function qiime dada2 denoise-single from Qiime2. This task starts by trimming and filtering sequences (see below) before joining paired reads to infer ASVs with DADA2 (The Divisive Amplicon Denoising Algorithm).

About trimming sequences:

It is convenient to ensure that paired-end reads overlap at least 12 nucleotides and that the quality of the reads does not fall below a PHRED score at 25 (corresponding to 1 incorrect base over a length of 320). To avoid problems in the determination of chimeras it is convenient to eliminate the first nucleotides as they may correspond to the primers that have been used in the 16S amplification.

truncated_reads_size refer to the position at which read sequences should be truncated due to decrease in quality. This truncates the 3' end of sequences (i.e. the right side).

5_prime_hard_trimming_reads_size refers to the position at which read sequences should be trimmed due to low quality. This trims the 5' end of the input sequences (i.e. the left side).

If both truncated_reads_size and 5_prime_hard_trimming_reads_size are provided, filtered reads will have length truncated_reads_size-5_prime_hard_trimming_reads_size.

Example

With the following sequence of 10 nucleotides ATCATCATCG, using truncated_reads_size at 8 and 5_prime_hard_trimming_reads_size at 2 will result in a sequence of 6 nucleotide CATCAT.

About Dada2:

Dada2 turns single-end sequences into merged, denoised, chimera-free, inferred sample sequences. The core denoising algorithm is built on a model of the errors in sequenced amplicon reads. For more information about Dada2, we suggest to read Benjamin J. Callahan et al., 2016 (https://www.nature.com/articles/nmeth.3869)

Input

Folder

Output

Feature frequency table
Table
2d excel like table
Rarefaction_curves
Rarefaction curves folder. Can be used with taxonomy task (!no rarefaction are done on counts!))

Configuration

threads

Optional

Number of threads

Type : intDefault value : 2

truncated_reads_size

Read size to conserve after quality PHRED check in the previous step

Type : int

5_prime_hard_trimming_reads_size

Optional

Read size to trim in 5prime

Type : int