Quick Start

This page gets you running BASALT in a few minutes.

Prerequisites

• Conda environment created (see Installation)
• Input files in the current working directory

Minimal Command

conda activate basalt_env
BASALT -a assembly.fasta -s sample_R1.fq,sample_R2.fq -t 32 -m 128

This runs the full pipeline (autobinning + refinement + reassembly) using default settings.

Common Workflows

Short-read onlyShort + Long readsShort + HiFi readsFast mode

BASALT -a as1.fa,as2.fa \
    -s s1_R1.fq,s1_R2.fq/s2_R1.fq,s2_R2.fq \
    -t 60 -m 250

BASALT -a as1.fa \
    -s sample_R1.fq,sample_R2.fq \
    -l nanopore.fastq \
    -t 60 -m 250

BASALT -a as1.fa \
    -s sample_R1.fq,sample_R2.fq \
    -hf hifi_reads.fastq \
    -t 32 -m 128

BASALT -a as1.fa \
    -s sample_R1.fq,sample_R2.fq \
    -t 32 -m 128 \
    --sensitive quick --refinepara quick

Input File Requirements

1. Place all input files in the working directory — BASALT does not support absolute paths.
2. Assembly files must be in FASTA format (.fa, .fna, .fasta).
3. Read files must be in FASTQ format (.fq, .fastq). Compressed files (.gz, .tar.gz, .zip) are automatically decompressed.
4. Each paired-end sample requires read pairs separated by ,. Multiple samples are separated by /.

Resuming a Run

BASALT uses checkpoints. If your run is interrupted:

BASALT --mode continue

For a fresh start (discarding previous progress):

BASALT -a assembly.fasta -s reads_R1.fq,reads_R2.fq -t 32 -m 128 --mode new

Expected Output

See the Output Files page for details on BASALT's output structure.

What's Next?

• Usage — full command-line reference
• Tutorial — step-by-step guide with demo data
• FAQ — common questions and answers