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Questions tagged [qiime]

QIIME is an open source software package for comparison and analysis of microbial communities.

QIIME (pronounced "chime") stands for Quantitative Insights Into Microbial Ecology. QIIME is an open source software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data (such as SSU rRNA) generated on a variety of platforms, but also supporting analysis of other types of data (such as shotgun metagenomic data). QIIME takes users from their raw sequencing output through initial analyses such as OTU picking, taxonomic assignment, and construction of phylogenetic trees from representative sequences of OTUs, and through downstream statistical analysis, visualization, and production of publication-quality graphics. QIIME has been applied to single studies based on billions of sequences from thousands of samples.

QIIME allows analysis of high-throughput community sequencing data.

63 questions
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remove the first 15 characters from every other line in a file

I have some txt files that look like this (they contain DNA sequences and sample…
colin
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Installing Qiime2 on Colab

Does anyone have any suggestions on how to install Qiime2 on Colab? I can't seem to get it to work with !pip install qiime2.
Timothy Kassis
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Converting biom to classic format?

Is it still possible to convert .biom tables from QIIME to QIIME’s "classic" OTU table format to use with Explicet? I've tried running the command from biom-format.org biom convert -i table.biom -o table.from_biom_w_taxonomy.txt --to-tsv…
nmshahir
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Adding a character string to every line in a file, incrementing that character string added by 1 each file

I have some set of files with character strings in lines such that there is a folder containing file1 file2 file3 and within those files there a variable length lists of strings of characters such that file 1 may…
colin
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I need to run a python script from php

I have to design a interface using PHP for a software written in python. Currently this software is used from command line by passing input, mostly the input is a text file. There are series of steps and for every step a python script is called.…
user1564657
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Why is my centred log ratio transformation on a distance matrix in R not symmetrical?

I am trying to transform a distance matrix from the qiime2 pathway using a centred log ratio in R. I uploaded the matrix directly from a qiime2 output file, and have converted to a data matrix and have checked that it is…
shannonevelyne
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Using Docker to install QIIME2

Can anyone help me figure out why it took around 20G of my C disk to install QIIME2 through Docker? Thank you! Before installing QIIME2, I had 30GB in my C disk, but only remains 8GB after installation.
Rowan
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Error: Aesthetics must be either length 1 or the same as the data (9): size

Im trying to plot my PCOA with qiime2R and ggplot2 since I find 2D UniFrac plots more informative than those given with Emperor in 3D. So I followed the qiime2R tutorial, but Im having trouble adding different aesthetics, I have seen other post but…
Jose Gracia Rodriguez
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Is it possible to add a conditional statement in snakemake's rule all?

I want to run multiple snakefiles called qc.smk , dada2.smk, picrust2.smkusing singularity. Then there is one snakefile called longitudinal.smk I would like to run conditionally. For example, if longitudinal data is being used. # set…
Noah_Seagull
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Is there any standard process for 16s rRNA analysis?

I'm trying to reproduce the dendogram results of this paper, concerning to an specific 16s rRNA analysis. But I don't know if there is a standard method for data management or data analysis. So, I've trying by myself. Below, a summary. In the…
Adonis Cedeño
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How to run qiime2 commands installed in miniconda from python 3.6 virtual environment

I have a flask application running in python 3.6 virtual environment and need to run qiime2 commands from this application. qiime2 is installed inside a miniconda virtual environment. My ubuntu has python 3.6 in /usr/bin, but "which python" returns:…
Liton
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How to use integers in subprocess.call

I am writing a program that runs qiime. I need the program to recognize numbers that the user types on the command line, but I think that subprocess.call may not be able to tell that the numbers are integers. What I have so far: # Items to…
Jessica
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bash: python: .py: command not found

I am trying to run the following command in QIIME2 virtual machine, installed on macbook but the code is not working validate_mapping_file.py -m Fasting_Map.txt -o mapping_output Here is the link: http://qiime.org/tutorials/tutorial.html I get the…
Muhammad Arslan
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Biom file v.1.0.0-dev created with biomformat not valid

I created a BIOM file, yyy.biom, using the functions make_biom and write_biom of the R package biomformat, version 1.2.0. yyy.biom looks like: "id":{}, "format":["Biological Observation Matrix…
Kense
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QIIME2 dada2 rlang.so error

I was running the QIIME2 moving picture tutorial, at the dada2 step, I was running: qiime dada2 denoise-single \ --i-demultiplexed-seqs demux.qza \ --p-trim-left 0 \ --p-trunc-len 120 \ --o-representative-sequences rep-seqs-dada2.qza…
user2762186
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