Main tool : dnappler
Full documentation: https://github.com/gbouras13/dnaapler
dnaapleris a simple python program that takes a single nucleotide input sequence (in FASTA format), finds the desired start gene using MMSeqs2, checks that the start codon of this gene is found, and if so, then reorients the chromosome to begin with this gene on the forward strand.
Note: As of v1.0.0, 'dnaapler' uses MMSeqs2 v13.45111 instead of BLAST for sequence alignment. MMSeqs2 is faster and compatible across platforms, including MacOS with Apple Silicon.
dnaapler has several commands for chromosomes, plasmids, and more.
Usage: dnaapler [OPTIONS] COMMAND [ARGS]...
Options:
-h, --help Show this message and exit.
-V, --version Show the version and exit.
Commands:
all Reorients contigs to begin with any of dnaA, repA, terL, or...
archaea Reorients your genome to begin with the archaeal COG1474...
bulk Reorients multiple genomes to begin with the same gene.
chromosome Reorients your genome to begin with the dnaA chromosomal...
citation Print the citation(s) for this tool.
custom Reorients your genome with a custom database.
mystery Reorients your genome with a random CDS.
nearest Reorients your genome to begin with the first CDS as...
phage Reorients your genome to begin with the terL large...
plasmid Reorients your genome to begin with the repA replication...
WARNING: Does not support multifasta files. Each sequence must be processed individually.
# Reorienting for a fasta of a chromsome sequence
dnaapler chromosome --input chromosome.fasta --output dnaapler_chr
# Reorienting for a fasta of a plasmid sequence
dnaapler plasmid --input plasmid.fasta --output dnaapler_plasmid
# Reorienting Mixed Contigs
dnaapler all -i input_mixed_contigs.fasta -o output_directory_path -p my_bacteria_name- biopython 1.78
- python 3.11.10
- pandas 2.2.2
- numpy 1.26.4
- mmseqs2 13.45111
- pyrodigal 3.6.3