Improves the taxonomic assignment of reads using barcode information of linked-reads data. The formats are built to be compatible with Kraken2, but any classifier can be used with a little reformatting.

1. A working pyhton3 installation
2. Standard unix commands awk and paste
3. ETE toolkit, intallable through conda
4. The first time you run cloudClassifier, you'll need an internet connexion to download the NCBI taxonomy

cloudClassifier needs two files as input:

1. The fastq of the linked reads, with barcodes marked with "BX:Z:" or "BC:Z:" tag. This fastq MUST be sorted by barcode. You can use the sort command on unix systems (with option -S for limiting memory usage)
2. The taxonomic classification of those reads, presented in the same order as the fastq file. Use the default Kraken2 output

cloudClassifier outputs a file in Kraken2 default output format, with improved taxonomic assignment.