An assortment of scripts to help process and automate various microbiome and metagenomic bioinformatic tools.
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gavinmdouglas Merge pull request #31 from gavinmdouglas/qiime2_fastq_sizes
BIOM fix and addition of script to get num reads in QIIME2 FASTQ files
Latest commit 4330e63 Jul 10, 2018
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.gitignore Add .gitignore Feb 4, 2015
LICENSE Create LICENSE Jul 18, 2017
README.md Added title to citation Jan 16, 2017
add_picrust_metadata.py added script to add metadata to picrust precalc file Sep 27, 2017
biom_to_stamp.py Add case to strip leading spaces in front of metadata fields Aug 12, 2015
chimera_filter.pl added check for whether db exists Jul 15, 2016
chimera_filter_usearch61.pl added chimera_filter_usearch61.pl, which is original version of chime… May 27, 2016
concat_lanes.pl concat scripts now check for _R1. as well as _R1_ and not for _1_ Jun 15, 2016
concat_paired_end.pl added check for _1.fastq PE syntax and now sample name is taken to be… Oct 5, 2017
convert_dada2_out.R removed dependency on biom R package and output in legacy TSV format Jul 10, 2018
count_fastq.pl Add new scripts May 19, 2015
create_qiime_map.pl Add script to create a qiime map.txt file Jan 23, 2015
dada2_chimera_taxa.R added random seed and allow taxa assignment skipping Oct 18, 2017
dada2_filter.R added check for non-numeric input parameters Sep 26, 2017
dada2_inference.R added OMEGA_A and BAND_SIZE options Nov 15, 2017
filter_fastq.pl Add new scripts May 19, 2015
filter_feature_table.R Added filter_feature_table.R Oct 24, 2017
fix_ITS2_spf.py fixed argparse typo in fix_ITS2_spf.py and only parsed for unidentifi… Jun 19, 2017
humann_stamp_to_biom.py added scripts to convert from HUMAnN and Metaphlan2 stamp to biom tsv Mar 31, 2017
humann_to_stamp.pl Make humann conversion more flexible Jan 22, 2015
merge_logfiles.R made optparse lines easier to read Sep 26, 2017
metaphlan2_stamp_to_biom.py added scripts to convert from HUMAnN and Metaphlan2 stamp to biom tsv Mar 31, 2017
metaphlan_to_stamp.pl Update to metaphlan2 Jan 30, 2015
parse_cutadapt_logs.py made parse_cutadapt_logs.py clarity changes and set input to be glob Sep 25, 2017
plot_metagenome_contributions.R added Unclassified as type of missing taxa Sep 27, 2017
qiime2_fastq_lengths.py added qiime2 script for getting number of reads in FASTQs in zipped f… Jul 10, 2018
read_filter.pl clarified that none is a possible option for primer_check Nov 16, 2016
remove_low_confidence_otus.py Added default cut-off to help documentation. Jul 10, 2018
run_contaminant_filter.pl Allow input files to be gzipped. Output will then be gzipped as well. Jul 20, 2017
run_deconseq.pl Add more wrapper scripts. Jan 20, 2015
run_fastq_to_fasta.pl added FASTX-Toolkit website Jan 18, 2017
run_kraken.pl added run_kraken.pl Jun 15, 2016
run_metaphlan.pl Fix file regular expression Dec 24, 2014
run_metaphlan2.pl changed bowtie2 default to be very-sensitive Nov 21, 2017
run_pear.pl made input filename more obvious in error Jan 31, 2018
run_pre_humann.pl updated help documentation for run_metaphlan2.pl and run_pre_humann.pl Mar 30, 2016
run_sra_to_fastq.pl Add wrapper script for fastq-dump from sra tookkit Mar 9, 2015
run_trimmomatic.pl added run_trimmomatic.pl check for gzipped files Mar 31, 2017

README.md

Microbiome Helper

An assortment of scripts to help process and automate various microbiome and metagenomic bioinformatic tools. We provide workflows, tutorials and a virtual box image to help researchers process microbial data.

Our paper on Microbiome Helper has been published in mSystems. Please cite this paper if you use our repository:

Comeau AM, Douglas GM, Langille MGI. 2017. Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research. mSystems 2(1): e00127-16; DOI: 10.1128/mSystems.00127-16    

Please see our wiki site for more info.

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