Summarize basecalling data from the sequencing_summary.txt file produced by albacore.

Change headers in fasta files to fit with kraken-build. Use NCBI-genome-download to download the genomes and use the assembly summary file from refseq to change to correct headers.

Extract sequences that map to a specific taxonomic id.

Usage

usage: extract_fastq_kraken.py [-h] --forward FORWARD [--reverse REVERSE]
                               --tax_id TAX_ID --kraken KRAKEN [--names NAMES]
                               [--nodes NODES] [--descendents] [--merge]
                               [--output OUTPUT]

Using --descendents will also extract all sequences within in this clade.
This requires the path to the names.dmp and nodes.dmp file used to build the kraken database. The --merge command will write all sequences to one fastq-file. To extract unclassified reads, use --tax_id 0.

Requirements

• seqtk
• pandas
• ncbiTaxonomyTree

Script to run pilon iteratively.

Run albacore basecalling when a new directory with reads is created.