hybracter Usage
hybracter install
You will first need to install the hybracter databases.
hybracter install
Alternatively, can also specify a particular directory to store them - you will need to specify this with -d <databases directory> when you run hybracter.
hybracter install -d <databases directory>
hybracter hybrid
You only need to specify a input CSV to run hybracter hybrid. It is recommended that you also specify an output directory with -o and a thread count with -t.
hybracter hybrid -i <input.csv> -o <output_dir> -t <threads> [other arguments]
Arguments
hybracter hybridrequires only a CSV file specified with-ior--input--no_polcawill turn off POLCA polishing with pypolca.- Use
--min_lengthto specify the minimum long-read length for Filtlong. - Use
--min_qualityto specify the minimum long-read quality for Filtlong. - You can specify a FASTA file containing contaminants with
--contaminants. All long reads that map to contaminants will be filtered out. - You can specify Escherichia phage lambda (a common contaminant in Nanopore library preparation) using
--contaminants lambda. --skip_qcwill skip all read QC steps.- You can change the
--medakaModel(all available options are listed inhybracter hybrid -h) - You can change the
--flyeModel(all available options are listed inhybracter hybrid -h) - You can turn off Medaka polishing using
--no_medaka- recommended for Q20+ modern Nanopore reads - You can turn off pypolca polishing using
--no_pypolca- I wouldn't though! - You can change the
--depth_filterfrom 0.25x chromosome coverage. This will filter out all Plassembler contigs below this depth. - By default,
hybracter hybridtakes the last polishing round as the final assembly (--logic last). We would not recommend changing this to--logic best, as picking the best polishing round according to ALE with--logic bestis not guaranteed to give the most accurate assembly (See our paper). - You can estimate the chromosome size with lrge by using
--auto- Note: if you have low quality long read sets (e.g. R9 FAST/HAC or sub Q15 reads), use
--autowith care. Users have reported that it can tend to overestimate the chromosome size with kmc - for lrge, some tests have shown similar (but not so bad) behaviour. This is not really solvable - it is simply a limitation of low quality data!
- Note: if you have low quality long read sets (e.g. R9 FAST/HAC or sub Q15 reads), use
- You can set a minimum long-read depth with
--min_depth. Hybracter will error out if your estimated long-reads coverage is lower than this. - If you are running hybracter on a Mac, please use
--mac(or find a Linux machine). This will make sure Medaka v1.8.0 is installed, as newer versions don't work on Macs. - From v0.10.0, Hybracter will implement the
--bacteriaflag designed specifically for bacterial genomes. See Ryan Wick's blogpost for some more explanation and benchmarking. If you do not want to use--bactera, please use--medaka_overrideto make sure hybracter uses your--medakaModel. This is likely most useful for R9 data. - If you have all your FASTQs in a certain directory, you can use
--datadirto specify these (and omit the directory path in the sample sheet--input). You can either specify 1 directory (if long and short FASTQs in the same directory) or 2 (long and short FASTQs in separate directories). If you specify 2, they must be separated by a comma e.g.--datadir "dirlong,dirshort".
hybracter version 0.9.0
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Usage: hybracter hybrid [OPTIONS] [SNAKE_ARGS]...
Run hybracter with hybrid long and paired end short reads
Options:
-i, --input TEXT Input csv [required]
--datadir TEXT Directory/ies where FASTQs are. Can specify
1 directory (long and short FASTQs in the
same directory) or 2 (long and short FASTQs
in separate directories). If you specify 2,
they must be separated by a comma e.g.
dirlong,dirshort. Will be added to the
filenames in the input csv.
--no_pypolca Do not use pypolca to polish assemblies with
short reads
--logic [best|last] Hybracter logic to select best assembly. Use
--last to pick the last polishing round. Use
--best to pick best assembly based on ALE
(hybrid). [default: last]
-o, --output PATH Output directory [default: hybracter_out]
--configfile TEXT Custom config file [default: config.yaml]
-t, --threads INTEGER Number of threads to use [default: 1]
--min_length INTEGER min read length for long reads [default:
1000]
--min_quality INTEGER min read quality score for long reads in bp.
[default: 9]
--skip_qc Do not run porechop_abi, filtlong and fastp
to QC the reads
-d, --databases PATH Plassembler Databases directory.
--subsample_depth INTEGER subsampled long read depth to subsample with
Filtlong. By default is 100x. [default:
100]
--min_depth INTEGER minimum long read depth to continue the run.
By default is 0x. Hybracter will error and
exit if a sample has less than
min_depth*chromosome_size bases of long-
reads left AFTER filtlong and porechop-ABI
steps are run. [default: 0]
--medakaModel [r1041_e82_400bps_sup_v5.0.0|r1041_e82_400bps_hac_v5.0.0|r1041_e82_400bps_hac_v4.3.0|r1041_e82_400bps_sup_v4.3.0|r1041_e82_400bps_hac_v4.2.0|r1041_e82_400bps_sup_v4.2.0|r941_sup_plant_g610|r941_min_fast_g507|r941_prom_fast_g507|r941_min_fast_g303|r941_min_high_g303|r941_min_high_g330|r941_prom_fast_g303|r941_prom_high_g303|r941_prom_high_g330|r941_min_high_g344|r941_min_high_g351|r941_min_high_g360|r941_prom_high_g344|r941_prom_high_g360|r941_prom_high_g4011|r10_min_high_g303|r10_min_high_g340|r103_min_high_g345|r103_min_high_g360|r103_prom_high_g360|r103_fast_g507|r103_hac_g507|r103_sup_g507|r104_e81_fast_g5015|r104_e81_sup_g5015|r104_e81_hac_g5015|r104_e81_sup_g610|r1041_e82_400bps_hac_g615|r1041_e82_400bps_fast_g615|r1041_e82_400bps_fast_g632|r1041_e82_260bps_fast_g632|r1041_e82_400bps_hac_g632|r1041_e82_400bps_sup_g615|r1041_e82_260bps_hac_g632|r1041_e82_260bps_sup_g632|r1041_e82_400bps_hac_v4.0.0|r1041_e82_400bps_sup_v4.0.0|r1041_e82_260bps_hac_v4.0.0|r1041_e82_260bps_sup_v4.0.0|r1041_e82_260bps_hac_v4.1.0|r1041_e82_260bps_sup_v4.1.0|r1041_e82_400bps_hac_v4.1.0|r1041_e82_400bps_sup_v4.1.0|r941_min_high_g340_rle|r941_min_hac_g507|r941_min_sup_g507|r941_prom_hac_g507|r941_prom_sup_g507|r941_e81_fast_g514|r941_e81_hac_g514|r941_e81_sup_g514]
Medaka Model. [default:
r1041_e82_400bps_sup_v5.0.0]
--flyeModel [--nano-hq|--nano-corr|--nano-raw|--pacbio-raw|--pacbio-corr|--pacbio-hifi]
Flye Assembly Parameter [default: --nano-
hq]
--contaminants PATH Contaminants FASTA file to map long
readsagainst to filter out. Choose
--contaminants lambda to filter out phage
lambda long reads.
--dnaapler_custom_db PATH Custom amino acid FASTA file of sequences to
be used as a database with dnaapler custom.
--no_medaka Do not polish the long read assembly with
Medaka.
--auto Automatically estimate the chromosome size
using KMC.
--depth_filter FLOAT Depth filter to pass to Plassembler. Filters
out all putative plasmid contigs below this
fraction of the chromosome read depth (needs
to be below in both long and short read sets
for hybrid).
--mac If you are running Hybracter on Mac -
installs v1.8.0 of Medaka as higher versions
break.
--medaka_override Use this if you do NOT want to use the
--bacteria option with Medaka. Instead your
specified --medakaModel will be used.
--extra_params_flye TEXT Use this if want to add extra parameters to
Flye.
--use-conda / --no-use-conda Use conda for Snakemake rules [default:
use-conda]
--conda-prefix PATH Custom conda env directory
--snake-default TEXT Customise Snakemake runtime args [default:
--rerun-incomplete, --printshellcmds,
--nolock, --show-failed-logs, --conda-
frontend mamba]
-h, --help Show this message and exit.
hybracter hybrid-single
You can also run a single isolate using the same input arguments as Unicycler by specifying hybracter hybrid-single. Instead of specifying a CSV with --input, use -l to specify the long read FASTQ file, -1 to specify the short read R1 file, -2 to specify the short read R2 file, -s to specify the sample name, -c to specify the chromosome size (-c can be omitted with --auto).
hybracter hybrid-single -l <longread FASTQ> -1 <R1 short reads FASTQ> -2 <R2 short reads FASTQ> -s <sample name> -c <chromosome size> -o <output_dir> -t <threads> [other arguments]
The other arguments are the same as hybracter hybrid
Usage: hybracter hybrid-single [OPTIONS] [SNAKE_ARGS]...
Run hybracter hybrid on 1 isolate
Options:
-l, --longreads TEXT FASTQ file of longreads [required]
-1, --short_one TEXT R1 FASTQ file of paired end short reads
[required]
-2, --short_two TEXT R2 FASTQ file of paired end short reads
[required]
-s, --sample TEXT Sample name. [default: sample]
-c, --chromosome INTEGER Approximate lower-bound chromosome length
(in base pairs). [default: 1000000]
--no_pypolca Do not use pypolca to polish assemblies with
short reads
--logic [best|last] Hybracter logic to select best assembly. Use
--best to pick best assembly based on ALE
(hybrid) or pyrodigal mean length (long).
Use --last to pick the last polishing round
regardless. [default: last]
-o, --output PATH Output directory [default: hybracter_out]
--configfile TEXT Custom config file [default: config.yaml]
-t, --threads INTEGER Number of threads to use [default: 1]
--min_length INTEGER min read length for long reads [default:
1000]
--min_quality INTEGER min read quality score for long reads in bp.
[default: 9]
--skip_qc Do not run porechop_abi, filtlong and fastp
to QC the reads
-d, --databases PATH Plassembler Databases directory.
--subsample_depth INTEGER subsampled long read depth to subsample with
Filtlong. By default is 100x. [default:
100]
--min_depth INTEGER minimum long read depth to continue the run.
By default is 0x. Hybracter will error and
exit if a sample has less than
min_depth*chromosome_size bases of long-
reads left AFTER filtlong and porechop-ABI
steps are run. [default: 0]
--medakaModel [r1041_e82_400bps_sup_v5.0.0|r1041_e82_400bps_hac_v5.0.0|r1041_e82_400bps_hac_v4.3.0|r1041_e82_400bps_sup_v4.3.0|r1041_e82_400bps_hac_v4.2.0|r1041_e82_400bps_sup_v4.2.0|r941_sup_plant_g610|r941_min_fast_g507|r941_prom_fast_g507|r941_min_fast_g303|r941_min_high_g303|r941_min_high_g330|r941_prom_fast_g303|r941_prom_high_g303|r941_prom_high_g330|r941_min_high_g344|r941_min_high_g351|r941_min_high_g360|r941_prom_high_g344|r941_prom_high_g360|r941_prom_high_g4011|r10_min_high_g303|r10_min_high_g340|r103_min_high_g345|r103_min_high_g360|r103_prom_high_g360|r103_fast_g507|r103_hac_g507|r103_sup_g507|r104_e81_fast_g5015|r104_e81_sup_g5015|r104_e81_hac_g5015|r104_e81_sup_g610|r1041_e82_400bps_hac_g615|r1041_e82_400bps_fast_g615|r1041_e82_400bps_fast_g632|r1041_e82_260bps_fast_g632|r1041_e82_400bps_hac_g632|r1041_e82_400bps_sup_g615|r1041_e82_260bps_hac_g632|r1041_e82_260bps_sup_g632|r1041_e82_400bps_hac_v4.0.0|r1041_e82_400bps_sup_v4.0.0|r1041_e82_260bps_hac_v4.0.0|r1041_e82_260bps_sup_v4.0.0|r1041_e82_260bps_hac_v4.1.0|r1041_e82_260bps_sup_v4.1.0|r1041_e82_400bps_hac_v4.1.0|r1041_e82_400bps_sup_v4.1.0|r941_min_high_g340_rle|r941_min_hac_g507|r941_min_sup_g507|r941_prom_hac_g507|r941_prom_sup_g507|r941_e81_fast_g514|r941_e81_hac_g514|r941_e81_sup_g514]
Medaka Model. [default:
r1041_e82_400bps_sup_v5.0.0]
--flyeModel [--nano-hq|--nano-corr|--nano-raw|--pacbio-raw|--pacbio-corr|--pacbio-hifi]
Flye Assembly Parameter [default: --nano-
hq]
--contaminants PATH Contaminants FASTA file to map long
readsagainst to filter out. Choose
--contaminants lambda to filter out phage
lambda long reads.
--dnaapler_custom_db PATH Custom amino acid FASTA file of sequences to
be used as a database with dnaapler custom.
--no_medaka Do not polish the long read assembly with
Medaka.
--auto Automatically estimate the chromosome size
using KMC.
--depth_filter FLOAT Depth filter to pass to Plassembler. Filters
out all putative plasmid contigs below this
fraction of the chromosome read depth (needs
to be below in both long and short read sets
for hybrid).
--mac If you are running Hybracter on Mac -
installs v1.8.0 of Medaka as higher versions
break.
--medaka_override Use this if you do NOT want to use the
--bacteria option with Medaka. Instead your
specified --medakaModel will be used.
--extra_params_flye TEXT Use this if want to add extra parameters to
Flye.
--use-conda / --no-use-conda Use conda for Snakemake rules [default:
use-conda]
--conda-prefix PATH Custom conda env directory
--snake-default TEXT Customise Snakemake runtime args [default:
--rerun-incomplete, --printshellcmds,
--nolock, --show-failed-logs, --conda-
frontend mamba]
-h, --help Show this message and exit.
hybracter long
You only need to specify a input CSV to run hybracter long. It is recommended that you also specify an output directory with -o and a thread count with -t.
hybracter long -i <input.csv> -o <output_dir> -t <threads> [other arguments]
Arguments
hybracter longrequires only a CSV file specified with-ior--input- Use
--min_lengthto specify the minimum long-read length for Filtlong. - Use
--min_qualityto specify the minimum long-read quality for Filtlong. - You can specify a FASTA file containing contaminants with
--contaminants. All long reads that map to contaminants will be filtered. - You can specify Escherichia phage lambda (a common contaminant in Nanopore library preparation) using
--contaminants lambda. --skip_qcwill skip all read QC steps.- You can change the
--medakaModel(all available options are listed inhybracter long -h) - You can change the
--flyeModel(all available options are listed inhybracter long -h) - You can turn off Medaka polishing using
--no_medaka- recommended for Q20+ modern Nanopore and PacBio reads - You can change the
--depth_filterfrom 0.25x chromosome coverage. This will filter out all Plassembler contigs below this depth. - You can force
hybracter longto pick the last polishing round (not the best according to pyrodigal mean CDS length) with--logic last.hybracter longdefaults to picking the best i.e.--logic best. - You can estimate the chromosome size with lrge by using
--auto- Note: if you have low quality long read sets (e.g. R9 FAST/HAC or sub Q15 reads), use
--autowith care. Users have reported that it can tend to overestimate the chromosome size with kmc - for lrge, some tests have shown similar (but not so bad) behaviour. This is not really solvable - it is simply a limitation of low quality data!
- Note: if you have low quality long read sets (e.g. R9 FAST/HAC or sub Q15 reads), use
- You can set a minimum long-read depth with
--min_depth. Hybracter will error out if your estimated long-reads coverage is lower than this. - If you are running hybracter on a Mac, please use
--mac(or find a Linux machine). This will make sure Medaka v1.8.0 is installed, as newer versions don't work on Macs. - From v0.10.0, Hybracter will implement the
--bacteriaflag designed specifically for bacterial genomes. See Ryan Wick's blogpost for some more explanation and benchmarking. If you do not want to use--bactera, please use--medaka_overrideto make sure hybracter uses your--medakaModel. This is likely most useful for R9 data. - If you have all your FASTQs in a certain directory, you can use
--datadirto specify these (and omit the directory path in the sample sheet--input).
Usage: hybracter long [OPTIONS] [SNAKE_ARGS]...
Run hybracter with only long reads
Options:
-i, --input TEXT Input csv [required]
--datadir TEXT Directory where FASTQs are. Will be added
to the filenames in the input csv.
-o, --output PATH Output directory [default: hybracter_out]
--configfile TEXT Custom config file [default: config.yaml]
-t, --threads INTEGER Number of threads to use [default: 1]
--min_length INTEGER min read length for long reads [default:
1000]
--min_quality INTEGER min read quality score for long reads in bp.
[default: 9]
--skip_qc Do not run porechop_abi, filtlong and fastp
to QC the reads
-d, --databases PATH Plassembler Databases directory.
--subsample_depth INTEGER subsampled long read depth to subsample with
Filtlong. By default is 100x. [default:
100]
--min_depth INTEGER minimum long read depth to continue the run.
By default is 0x. Hybracter will error and
exit if a sample has less than
min_depth*chromosome_size bases of long-
reads left AFTER filtlong and porechop-ABI
steps are run. [default: 0]
--medakaModel [r1041_e82_400bps_sup_v5.0.0|r1041_e82_400bps_hac_v5.0.0|r1041_e82_400bps_hac_v4.3.0|r1041_e82_400bps_sup_v4.3.0|r1041_e82_400bps_hac_v4.2.0|r1041_e82_400bps_sup_v4.2.0|r941_sup_plant_g610|r941_min_fast_g507|r941_prom_fast_g507|r941_min_fast_g303|r941_min_high_g303|r941_min_high_g330|r941_prom_fast_g303|r941_prom_high_g303|r941_prom_high_g330|r941_min_high_g344|r941_min_high_g351|r941_min_high_g360|r941_prom_high_g344|r941_prom_high_g360|r941_prom_high_g4011|r10_min_high_g303|r10_min_high_g340|r103_min_high_g345|r103_min_high_g360|r103_prom_high_g360|r103_fast_g507|r103_hac_g507|r103_sup_g507|r104_e81_fast_g5015|r104_e81_sup_g5015|r104_e81_hac_g5015|r104_e81_sup_g610|r1041_e82_400bps_hac_g615|r1041_e82_400bps_fast_g615|r1041_e82_400bps_fast_g632|r1041_e82_260bps_fast_g632|r1041_e82_400bps_hac_g632|r1041_e82_400bps_sup_g615|r1041_e82_260bps_hac_g632|r1041_e82_260bps_sup_g632|r1041_e82_400bps_hac_v4.0.0|r1041_e82_400bps_sup_v4.0.0|r1041_e82_260bps_hac_v4.0.0|r1041_e82_260bps_sup_v4.0.0|r1041_e82_260bps_hac_v4.1.0|r1041_e82_260bps_sup_v4.1.0|r1041_e82_400bps_hac_v4.1.0|r1041_e82_400bps_sup_v4.1.0|r941_min_high_g340_rle|r941_min_hac_g507|r941_min_sup_g507|r941_prom_hac_g507|r941_prom_sup_g507|r941_e81_fast_g514|r941_e81_hac_g514|r941_e81_sup_g514]
Medaka Model. [default:
r1041_e82_400bps_sup_v5.0.0]
--flyeModel [--nano-hq|--nano-corr|--nano-raw|--pacbio-raw|--pacbio-corr|--pacbio-hifi]
Flye Assembly Parameter [default: --nano-
hq]
--contaminants PATH Contaminants FASTA file to map long
readsagainst to filter out. Choose
--contaminants lambda to filter out phage
lambda long reads.
--dnaapler_custom_db PATH Custom amino acid FASTA file of sequences to
be used as a database with dnaapler custom.
--no_medaka Do not polish the long read assembly with
Medaka.
--auto Automatically estimate the chromosome size
using KMC.
--depth_filter FLOAT Depth filter to pass to Plassembler. Filters
out all putative plasmid contigs below this
fraction of the chromosome read depth (needs
to be below in both long and short read sets
for hybrid).
--mac If you are running Hybracter on Mac -
installs v1.8.0 of Medaka as higher versions
break.
--medaka_override Use this if you do NOT want to use the
--bacteria option with Medaka. Instead your
specified --medakaModel will be used.
--extra_params_flye TEXT Use this if want to add extra parameters to
Flye.
--use-conda / --no-use-conda Use conda for Snakemake rules [default:
use-conda]
--conda-prefix PATH Custom conda env directory
--snake-default TEXT Customise Snakemake runtime args [default:
--rerun-incomplete, --printshellcmds,
--nolock, --show-failed-logs, --conda-
frontend mamba]
--logic [best|last] Hybracter logic to select best assembly. Use
--best to pick best assembly based on ALE
(hybrid) or pyrodigal mean length (long).
Use --last to pick the last polishing round
regardless. [default: best]
-h, --help Show this message and exit.
hybracter long-single
Run hybracter long on a single isolate. Instead of specifying a CSV with --input, use -l to specify the long read FASTQ file, -s to specify the sample name, -c to specify the chromosome size (unless you are using --auto, then you don't need to specify -c).
hybracter long-single -l <longread FASTQ> -s <sample name> -c <chromosome size> -o <output_dir> -t <threads> [other arguments]
Usage: hybracter long-single [OPTIONS] [SNAKE_ARGS]...
Run hybracter long on 1 isolate
Options:
-l, --longreads TEXT FASTQ file of longreads [required]
-s, --sample TEXT Sample name. [default: sample]
-c, --chromosome INTEGER FApproximate lower-bound chromosome length
(in base pairs). [default: 1000000]
-o, --output PATH Output directory [default: hybracter_out]
--configfile TEXT Custom config file [default: config.yaml]
-t, --threads INTEGER Number of threads to use [default: 1]
--min_length INTEGER min read length for long reads [default:
1000]
--min_quality INTEGER min read quality score for long reads in bp.
[default: 9]
--skip_qc Do not run porechop_abi, filtlong and fastp
to QC the reads
-d, --databases PATH Plassembler Databases directory.
--subsample_depth INTEGER subsampled long read depth to subsample with
Filtlong. By default is 100x. [default:
100]
--min_depth INTEGER minimum long read depth to continue the run.
By default is 0x. Hybracter will error and
exit if a sample has less than
min_depth*chromosome_size bases of long-
reads left AFTER filtlong and porechop-ABI
steps are run. [default: 0]
--medakaModel [r1041_e82_400bps_sup_v5.0.0|r1041_e82_400bps_hac_v5.0.0|r1041_e82_400bps_hac_v4.3.0|r1041_e82_400bps_sup_v4.3.0|r1041_e82_400bps_hac_v4.2.0|r1041_e82_400bps_sup_v4.2.0|r941_sup_plant_g610|r941_min_fast_g507|r941_prom_fast_g507|r941_min_fast_g303|r941_min_high_g303|r941_min_high_g330|r941_prom_fast_g303|r941_prom_high_g303|r941_prom_high_g330|r941_min_high_g344|r941_min_high_g351|r941_min_high_g360|r941_prom_high_g344|r941_prom_high_g360|r941_prom_high_g4011|r10_min_high_g303|r10_min_high_g340|r103_min_high_g345|r103_min_high_g360|r103_prom_high_g360|r103_fast_g507|r103_hac_g507|r103_sup_g507|r104_e81_fast_g5015|r104_e81_sup_g5015|r104_e81_hac_g5015|r104_e81_sup_g610|r1041_e82_400bps_hac_g615|r1041_e82_400bps_fast_g615|r1041_e82_400bps_fast_g632|r1041_e82_260bps_fast_g632|r1041_e82_400bps_hac_g632|r1041_e82_400bps_sup_g615|r1041_e82_260bps_hac_g632|r1041_e82_260bps_sup_g632|r1041_e82_400bps_hac_v4.0.0|r1041_e82_400bps_sup_v4.0.0|r1041_e82_260bps_hac_v4.0.0|r1041_e82_260bps_sup_v4.0.0|r1041_e82_260bps_hac_v4.1.0|r1041_e82_260bps_sup_v4.1.0|r1041_e82_400bps_hac_v4.1.0|r1041_e82_400bps_sup_v4.1.0|r941_min_high_g340_rle|r941_min_hac_g507|r941_min_sup_g507|r941_prom_hac_g507|r941_prom_sup_g507|r941_e81_fast_g514|r941_e81_hac_g514|r941_e81_sup_g514]
Medaka Model. [default:
r1041_e82_400bps_sup_v5.0.0]
--flyeModel [--nano-hq|--nano-corr|--nano-raw|--pacbio-raw|--pacbio-corr|--pacbio-hifi]
Flye Assembly Parameter [default: --nano-
hq]
--contaminants PATH Contaminants FASTA file to map long
readsagainst to filter out. Choose
--contaminants lambda to filter out phage
lambda long reads.
--dnaapler_custom_db PATH Custom amino acid FASTA file of sequences to
be used as a database with dnaapler custom.
--no_medaka Do not polish the long read assembly with
Medaka.
--auto Automatically estimate the chromosome size
using KMC.
--depth_filter FLOAT Depth filter to pass to Plassembler. Filters
out all putative plasmid contigs below this
fraction of the chromosome read depth (needs
to be below in both long and short read sets
for hybrid).
--mac If you are running Hybracter on Mac -
installs v1.8.0 of Medaka as higher versions
break.
--medaka_override Use this if you do NOT want to use the
--bacteria option with Medaka. Instead your
specified --medakaModel will be used.
--extra_params_flye TEXT Use this if want to add extra parameters to
Flye.
--use-conda / --no-use-conda Use conda for Snakemake rules [default:
use-conda]
--conda-prefix PATH Custom conda env directory
--snake-default TEXT Customise Snakemake runtime args [default:
--rerun-incomplete, --printshellcmds,
--nolock, --show-failed-logs, --conda-
frontend mamba]
--logic [best|last] Hybracter logic to select best assembly. Use
--best to pick best assembly based on ALE
(hybrid) or pyrodigal mean length (long).
Use --last to pick the last polishing round
regardless. [default: best]
-h, --help Show this message and exit.