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Publication Year: 2023

1 to 10 of 22 Results

fastqCombinePairedEnd.py 1 mars 2024 - Original data for " Chapuis MP et al. (2023). Evaluation of 96-well high-throughput DNA extraction methods for 16S rRNA gene metabarcoding. Molecular Ecology Resources, 23, 1509–1525" Python Source Code - 4,1 KB - MD5: a8615acfbf0737600ce065ffb8c8b83f Executable file required for using the Shell script "Preprocess_1step_forFrogs.sh"
Preprocess_1step_forFrogs.sh 1 mars 2024 - Original data for " Chapuis MP et al. (2023). Evaluation of 96-well high-throughput DNA extraction methods for 16S rRNA gene metabarcoding. Molecular Ecology Resources, 23, 1509–1525" Shell Script - 13,2 KB - MD5: 930c4ed891ebdbdcccfab0b01dd893b5 Shell script for preprocessing of raw sequences (before running Frogs) : From demultiplexed fastq.gz files produced from an Illumina MiSeq amplicon library, this script cuts reads from 3' primers (with cutadapt), trims on length longer reads (with fastx_trimmer), then merges read...
remove_void.awk 1 mars 2024 - Original data for " Chapuis MP et al. (2023). Evaluation of 96-well high-throughput DNA extraction methods for 16S rRNA gene metabarcoding. Molecular Ecology Resources, 23, 1509–1525" application/x-awk - 329 B - MD5: 3e02ca2e3e65e7294e2e88d9033006eb Executable file required for using the Shell script "Preprocess_1step_forFrogs.sh"
SANDMAN7.3.nlogo 2 oct. 2023 - Multi-agent model SANDMAN: source code Unknown - 75,6 KB - MD5: 48f806a08ad63521fa3927f7ad8a1f53 Code V7.3. Source code suitable for Netlogo 6.3.0
Filter1_sequencing-run.R 2 mai 2023 - Original data for " Chapuis MP et al. (2023). Evaluation of 96-well high-throughput DNA extraction methods for 16S rRNA gene metabarcoding. Molecular Ecology Resources, 23, 1509–1525" R Syntax - 8,3 KB - MD5: 14dd967c52750f012e387f2c3c786a35 First R script for data filtering. This script filter data for index contamination following correction 2 from Galan et al. 2016 (Tfa) and works on an abundance text file from Frogs and a metadata file that specifies sample names, biological units, technical replicates and contro...
Filtering_Functions.R 2 mai 2023 - Original data for " Chapuis MP et al. (2023). Evaluation of 96-well high-throughput DNA extraction methods for 16S rRNA gene metabarcoding. Molecular Ecology Resources, 23, 1509–1525" R Syntax - 377 B - MD5: 7cc002154f0e34a37b6b53f1ad649fb4 Loading packages and functions required for R scripts for data filtering.
Nextfilters_and_reduction.R 2 mai 2023 - Original data for " Chapuis MP et al. (2023). Evaluation of 96-well high-throughput DNA extraction methods for 16S rRNA gene metabarcoding. Molecular Ecology Resources, 23, 1509–1525" R Syntax - 20,2 KB - MD5: 2ea6d5266bd97ee5195e4feff7a93b3a Second R script for data filtering. This script keeps positive data only if congruent between replicates (duplicates or triplicates) and filters data for extraction & pcr contamination following correction 1 from Galan et al. 2016 (Tcc) and using negative controls. It works on an...
Preprocess_1step_forFrogs_parameters_file_16Sv4.txt 2 mai 2023 - Original data for " Chapuis MP et al. (2023). Evaluation of 96-well high-throughput DNA extraction methods for 16S rRNA gene metabarcoding. Molecular Ecology Resources, 23, 1509–1525" Plain Text - 3,5 KB - MD5: 8a32246bf8d40f71976a9131e37a0ac1 This text file contain parameters needed by the shell script "Preprocess_1step_forFrogs.sh"
R-analyses.R 2 mai 2023 - Original data for " Chapuis MP et al. (2023). Evaluation of 96-well high-throughput DNA extraction methods for 16S rRNA gene metabarcoding. Molecular Ecology Resources, 23, 1509–1525" R Source Code - 20,9 KB - MD5: 775e2f0bad561c40e36b19d1ec9219e0 R script for all statistical analyses (using R-data.xlsx).
R-data.tab 2 mai 2023 - Original data for " Chapuis MP et al. (2023). Evaluation of 96-well high-throughput DNA extraction methods for 16S rRNA gene metabarcoding. Molecular Ecology Resources, 23, 1509–1525" Tabular Data - 4,1 KB - 49 Variables, 17 Observations - UNF:6:3cpS5HiYLk+POaq90NQuug== Data for statistical analyses for each HTP 96 DNA purification method and cell community standard (DNA yield and abundance tables from amplicon sequencing of the V4 region of bacterial 16SrRNA gene, with metadata)

fastqCombinePairedEnd.py

1 mars 2024 - Original data for " Chapuis MP et al. (2023). Evaluation of 96-well high-throughput DNA extraction methods for 16S rRNA gene metabarcoding. Molecular Ecology Resources, 23, 1509–1525"

Python Source Code - 4,1 KB -

Executable file required for using the Shell script "Preprocess_1step_forFrogs.sh"

Preprocess_1step_forFrogs.sh

1 mars 2024 - Original data for " Chapuis MP et al. (2023). Evaluation of 96-well high-throughput DNA extraction methods for 16S rRNA gene metabarcoding. Molecular Ecology Resources, 23, 1509–1525"

Shell Script - 13,2 KB -

Shell script for preprocessing of raw sequences (before running Frogs) : From demultiplexed fastq.gz files produced from an Illumina MiSeq amplicon library, this script cuts reads from 3' primers (with cutadapt), trims on length longer reads (with fastx_trimmer), then merges read...

remove_void.awk

1 mars 2024 - Original data for " Chapuis MP et al. (2023). Evaluation of 96-well high-throughput DNA extraction methods for 16S rRNA gene metabarcoding. Molecular Ecology Resources, 23, 1509–1525"

application/x-awk - 329 B -

Executable file required for using the Shell script "Preprocess_1step_forFrogs.sh"

SANDMAN7.3.nlogo

2 oct. 2023 - Multi-agent model SANDMAN: source code

Unknown - 75,6 KB -

Code

V7.3. Source code suitable for Netlogo 6.3.0

Filter1_sequencing-run.R

2 mai 2023 - Original data for " Chapuis MP et al. (2023). Evaluation of 96-well high-throughput DNA extraction methods for 16S rRNA gene metabarcoding. Molecular Ecology Resources, 23, 1509–1525"

R Syntax - 8,3 KB -

First R script for data filtering. This script filter data for index contamination following correction 2 from Galan et al. 2016 (Tfa) and works on an abundance text file from Frogs and a metadata file that specifies sample names, biological units, technical replicates and contro...

Filtering_Functions.R

2 mai 2023 - Original data for " Chapuis MP et al. (2023). Evaluation of 96-well high-throughput DNA extraction methods for 16S rRNA gene metabarcoding. Molecular Ecology Resources, 23, 1509–1525"

R Syntax - 377 B -

Loading packages and functions required for R scripts for data filtering.

Nextfilters_and_reduction.R

2 mai 2023 - Original data for " Chapuis MP et al. (2023). Evaluation of 96-well high-throughput DNA extraction methods for 16S rRNA gene metabarcoding. Molecular Ecology Resources, 23, 1509–1525"

R Syntax - 20,2 KB -

Second R script for data filtering. This script keeps positive data only if congruent between replicates (duplicates or triplicates) and filters data for extraction & pcr contamination following correction 1 from Galan et al. 2016 (Tcc) and using negative controls. It works on an...

Preprocess_1step_forFrogs_parameters_file_16Sv4.txt

2 mai 2023 - Original data for " Chapuis MP et al. (2023). Evaluation of 96-well high-throughput DNA extraction methods for 16S rRNA gene metabarcoding. Molecular Ecology Resources, 23, 1509–1525"

Plain Text - 3,5 KB -

This text file contain parameters needed by the shell script "Preprocess_1step_forFrogs.sh"

R-analyses.R

2 mai 2023 - Original data for " Chapuis MP et al. (2023). Evaluation of 96-well high-throughput DNA extraction methods for 16S rRNA gene metabarcoding. Molecular Ecology Resources, 23, 1509–1525"

R Source Code - 20,9 KB -

R script for all statistical analyses (using R-data.xlsx).

R-data.tab

2 mai 2023 - Original data for " Chapuis MP et al. (2023). Evaluation of 96-well high-throughput DNA extraction methods for 16S rRNA gene metabarcoding. Molecular Ecology Resources, 23, 1509–1525"

Tabular Data - 4,1 KB - 49 Variables, 17 Observations -

Data for statistical analyses for each HTP 96 DNA purification method and cell community standard (DNA yield and abundance tables from amplicon sequencing of the V4 region of bacterial 16SrRNA gene, with metadata)

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