To activate this environment, use
conda activate BASALT
To deactivate an active environment, use
conda deactivate
if you have a single assembly:
BASALT -a assembly.fasta -s short.R1.fq,short.R2.fq -l nanopore.fastq -t 60 -m 230
if you have multiple assemblies:
BASALT -a assembly1.fasta,assembly2.fasta -s short1.R1.fq,short1.R2.fq/short2.R1.fq,short2.R2.fq -l nanopore1.fastq,nanopore2.fastq -t 60 -m 230
You may enter as mang assemblies as you wish, or as many short-reads or long-rads as you wish.
Input data:
-a ASSEMBLIES, --assemblies ASSEMBLIES List of assemblies, e.g.: as1.fa,as2.fa
-s --shortreads SR_DATASETS List of paired-end reads, e.g.:r1_1.fq,r1_2.fq/r2_1.fq,r2_2.fq (paried_ends reads need '/' to seperate)
Optional parameters:
-h show this help message and exit
-l LONG_DATASETS, --longreads LONG_DATASETS List of long reads, e.g.: lr1.fq,lr2.fq
-e EXTRA_BINNER, --extra_binner EXTRA_BINNER. Extra binner for binning: m: metabinner, v: vamb; for instance: -e m, means BASALT will use metabinner for binning besides metabat2, maxbin2, and concoct
-c HI_C_DATASET, --HIC HI_C_DATASET. List of Hi-C dataset(s), e.g.: hc1.fq,hc2.fq
-t Number of threads. For example, -t 120. Default thread is set at 2.
-m Maximum memory limit at gigabytes (GB). For example, -r 750. Default memory limit is set at 64GB. The maximum memory limit is critical for reassembly.
--mode RUNNING_MODE Start a new project (new) or continue to run (continue). e.g. --mode continue / --mode new
--module FUNCTIONAL_MODULE Three modules: 1. autobinning; 2. refinement; 3. reassembly. Default will run all modules. But you could set the only perform modle. e.g. --module reassembly
--autopara AUTOBINING_PARAMETERS Three parameters to chose: 1. more-sensitive; 2.sensitive; 3. quick. Default: more-sensitive. e.g. --autopara sensitive
--refinepara REFINEMENT_PARAMTER Two refinement parameters to chose: 1. deep; 2. quick. Default: deep. e.g. --refinepara quick
--max-ctn Contamination cutoff in the refinement step. Default cutoff is set at 20, which means BASALT will only refine those bins with contamination at 20 or below.
--min-cpn Completeness cutoff in the refinement step. Default cutoff is set at 35, which means BASALT will only refine those bins with completeness at 35 or above.
Note:
If you encounter an error during use the BASALT, try to resubmit the task.