1.2.2

HoCoRT

Main tool: HoCoRT v1.2.2 Dependencies:
bwa-mem2 v2.2.1 histat2 v2.2.1 sparsehash v2.0.4 sdsl-lite v2.1.1 btl_bloomfilter v1.2.1 biobloom v2.3.5

Code repository: https://github.com/ignasrum/hocort

Basic information on how to use this tool:

• executable: |

hocort --help
usage: hocort [subcommand] [options]

hocort: remove specific organisms from sequencing reads

optional arguments:
  -h, --help     show this help message and exit
  -v, --version  flag: print version

available subcommands:
  subcommand
    map          map reads to a reference genome and output mapped/unmapped reads
    index        build index/-es for supported tools

• help: hocort --help
• version: hocort --version
• description: |

Remove specific organisms from sequencing reads.

Full documentation: https://github.com/ignasrum/hocort/wiki

Testing HoCoRT analysis

curl -L -o test/genome.fna https://raw.githubusercontent.com/ignasrum/hocort/main/tests/test_data/fasta/genome.fna

hocort index \
  bowtie2 \
  --input test/genome.fna \
  --output test/hocort_test