Metagenomic Amplicon analysis pipeline
Collection of helper scripts for amplicon sequence analysis, e.g. as outlined in the workflow in the docs directory.
Download and documentation
For download please visit the official ampli-tools github repository page.
Content
docs/amplicon_pipeline.pdf
This pdf outlines the amplicon analysis workflow used and taught by c3 researchers.
addSampleQualByFastq.pl
Script to add qualifier “sample” to fasta header to be able to use a fasta file with Qiime.
usage: addSamplQualByFasta -q FASTQ_DIR -f FASTA_FILE -o OUTPUT_FILE -m MAPPING_FILE
batchCountFastqSeqs.pl
Script to count sequences of all fastq files in given directory. Prints out a list of “filename: SEQ_NUM” Additionally performs basic check of correct format, i.e., checks that number of line is a multiple of 4
usage: batchCountFastqSeqs.pl -d FASTQ_DIRECTORY
batchRenameFiles.pl
Script to rename all files in a directory. It splits all files of given extension at a given separator and concatenates a given number of split segments to a new file name.
usage: batchRenameFiles.pl -d INPUT_FILE_DIRECTORY -f NUMBER_OF_SEGMETNS_TO_KEEP -e FILE_EXTENSION
convert_to_qiime.pl
Script to convert the output of addSampleQualByFastq.pl to Qiime split_libraries output (e.g. for use with picrust).
usage: convert_to_qiime.pl -i INPUT_FASTA_FILE -o OUTPUT_FASTA_FILE
demultiplex.pl
Simple demultiplexing script for dual barcode single-end reads of structure:
BARCODE (fw) - PRIMER (fw) - INSERT - PRIMER (rv) - BARCODE (rv) - ILLUMINA PRIMER
usage: demultiplex [-c -f] -i FASTQ -m MOTHUR_OLIGOS -o OUTPUT_DIR
extract_seqs_from_aln.pl
Script to extract sequences in given un-aligned fasta file from aligned fasta file
usage: extract_seqs_from_aln.pl -i ALIGNED_INPUT_FASTA_FILE -o ALIGNED_OUTPUT_FASTA_FILE -f UNALIGNED_FASTA_FILE
extract_seqs_from_fasta.pl
Script to extract sequences form a fasta file based on a given list.
usage: -i INPUT_FASTA_FILE -o OUTPUT_FASTA_FILE -l SEQUENCE_LIST