flosz / qzip Goto Github PK

prerequisites:
- biom 2.1.6
- trimmomatic 0.38
- cutadapt 1.17
- swarm 2.2.2
- vsearch 2.8.2
- mothur 1.40.5
- parallel 20141022
- mafft
- RaxML

installing:
git clone https://github.com/PyoneerO/qzip
copy q-zip_commands.sh and q-zip_parameters.txt into your working directory.

input:
- demultiplexed Miseq paired-end raw data
- sample metadata file (optional)

naming scheme:
exemplary raw file name
<sequencing date>_<machine id><run id><sample id><well id/alternative sample id><lane id><read id>_001.fastq.gz
180201_M00758_0705_lane1nifh10_S39_L001_R1_001.fastq.gz

the sample names for your sample metadata mapping require the following scheme 
(according to the corresponding raw sequence files without the segment "_<lane id><read id>_001.fastq.gz"):

<sample id> (lane1nifh10) or
<sample id><well id/alternative sample id> (lane1nifh10_S39) or
<sequencing date>_<machine id><run id><sample id><well id/alternative sample id> (80201_M00758_0705_lane1nifh10_S39)

If you provide regular expressions for Prefix (<sequencing date>_<machine id><run id>_) and Suffix 
(_<well id/alternative sample id>) in the parameter file, the sample names in the OTU tables will be cleaned from them.

parameter:
open the file q-zip_parameters.txt with an editor and set parameters especially for:
- primer sequences
- reference sets
- paths to the needed executables

workflow execution:
simply source the script by . ./q-zip_commands.sh

output:
q-zip_commands.sh - used workflow file
q-zip_parameters.txt - used parameter file
q-zip_seq_of_coms.txt - sequence of used commands, sourcing of this file should result produce reproducible results
q-zip_workflow.log - log file
refDB.zip - primer filtered and trimmed reference set
seq_number_stats.txt - sequence number and length statistics for the preprocessing steps
amplicon_table.csv - distribution table of amplicons in samples
swarm.seeds.no.singletons - swarm/OTU representing sequences (singleton removal applied by default!)
swarm.swarm.no.singletons - list of amplicons per swarm/OTU (singleton removal applied by default!)
<project id>_observation_metadata_full.map - OTU/observation metadata
<project id>_sample_metadata.map - sample metadata
<project id>_OTU_table_full_json_clean.biom - OTU table as biom, json format, all provided metadata included
<project id>_OTU_table_full_hdf5_clean.biom - OTU table as biom, hdf5 format, all provided metadata included
<project id>_9_OTU_table_pure_clean.csv - OTU table + taxonomie as csv