conda create -n toxin python=3
conda activate toxin
conda install BtToxin_scanner

BtToxin_scanner [Options]

[--help]                      Print the help message and exit

[--version]                   Show version number of BtToxin_scanner and exit

[--threads (INT)]             Number of threads to be used ( Default 4 )

[--SeqPath (PATH)]            [Required] The path of input sequences ( Default "the current directory" )

[--SequenceType (STRING)]     [Required] Sequence type for inputs. "reads", "nucl", "orfs", and "prot" avaliable ( Default nucl )

[--platform (STRING)]         [Required] Sequencing Platform, "illumina", "pacbio", "oxford" and "hybrid" available ( Default illumina )

[--assemble_only (STRING)]    Only perform genome assembly without predicting toxins.

[--reads1 (STRING)]           [Required by "reads"] The suffix name of reads 1 ( for example: if the name of reads 1 is "YBT-1520_L1_I050.R1.clean.fastq.gz", "YBT-1520" is the strain same, so the suffix name should be ".R1.clean.fastq.gz" )

[--reads2 (STRING)]           [Required by "reads"] The suffix name of reads 2( not required by "oxford" and "pacbio". For example: if the name of reads 2 is "YBT-1520_2.fq", the suffix name should be _2.fq" )

[--suffix_len (INT)]          [Required by "reads"] (Strongly recommended) The suffix length of the reads file, that is the length of the reads name minus the length of the strain name. For example the --suffix_len of "YBT-1520_L1_I050.R1.clean.fastq.gz" is 26 ( "YBT-1520" is the strain name ) ( Default 0 )

[--short1 (STRING)]           [Required] FASTQ file of first short reads in each pair. Needed by hybrid assembly ( Default Unset )

[--short2 (STRING)]           [Required] FASTQ file of second short reads in each pair. Needed by hybrid assembly ( Default Unset )

[--long (STRING)]             [Required] FASTQ or FASTA file of long reads. Needed by hybrid assembly ( Default Unset )

[--hout (STRING)]             [Required] Output directory for hybrid assembly ( Default "../../Results/Assembles/Hybrid" )

[--genomeSize (STRING)]       [Required] An estimate of the size of the genome. Common suffixes are allowed, for example, 3.7m or 2.8g. Needed by PacBio data and Oxford data ( Default 6.07m )

[--Scaf_suffix (STRING)]      The suffix of scaffolds or genomes ( Default ".filtered.fas" )

[--orfs_suffix (STRING)]      The suffix of orfs files ( Default ".ffn" )

[--prot_suffix (STRING)]      The suffix of protein files ( Default ".faa" )

BtToxin_scanner --SeqPath <Illumina Reads PATH> --SequenceType reads --platform illumina --reads1 <suffix name of reads 1> -reads2 <suffix name of reads 2> --threads <INT> --suffix_len <INT>

BtToxin_scanner --SeqPath <PacBio Reads PATH> --SequenceType reads --platform pacbio --reads1 <suffix name of PacBio reads> --threads <INT> --suffix_len <INT>

BtToxin_scanner --SeqPath <Oxford Reads PATH> --SequenceType reads --platform oxford --reads1 <suffix name of Oxford reads> --threads <INT> --suffix_len <INT>

BtToxin_scanner --SeqPath <Reads PATH> --SequenceType reads --platform hybrid --short1 <short reads 1> --short2 <short reads 2> --long <long reads> --threads <INT>

BtToxin_scanner --SeqPath <Assembled genome PATH> --SequenceType nucl --Scaf_suffix <suffix of genomes> --threads <INT>

BtToxin_scanner --SeqPath <Protein file PATH> --SequenceType prot --prot_suffix <suffix of protein files> --threads <INT>

BtToxin_scanner --SeqPath <orfs file PATH> --SequenceType orfs --orfs_suffix <suffix of orfs files> --threads <INT>