Microbial Genomics Lab's repositories
OTUsamples2krona
Simple script to generate Krona charts for all samples in an OTU table file
coverage_calculator
A simple script to calculate the coverage of a genome assembly
basic_stats
Basic fasta statistics
db_reformatter
Script to reformat the EzBioCloud database to be used with mg_classifier
chimera_detector
A simple script to detect chimeric sequences in 16S/18S metagenomic samples.
diversity_indexes
Calculation of basic ecological diversity indexes from a list of values
fasta_cleaner
A bash script to rename and clean multifasta files
metagenomic_pipeline
Description of the metagenomic pipeline we have for analysis of 16S and 18S amplicon NGS
nextera_cleaner
Script to clean Illumina pair-end sequences produced with the Nextera kit. Bases below Q30, Ns, and Nextera adapters are removed. Bases can also be removed at the beginning and end of each sequence. At the end, clean files can be analyzed with FastQC.
pair-end_cleaner
Script to unzip, clean, assemble, and convert illumina pair-end fastq files in all subdirectories for 16S amplicon data (V3, V4 and V3-V4 regions).
fasta_header_renamer
Script to rename the headers of a mutifasta file with the name of the file, it also adds a consecutive number to each sequence header.
fasta_renamer
Script to rename the headers of a multifasta file or files. A consecutive number will be added to each sequence header (>header_1, >header_2, etc.)
mg_classifier
Super fast script for classifying metagenomic 16S/18S sequences