Build index

Use bsbit index to build the complete alignment index from a reference genome FASTA:

bsbit index \
  -r GRCh38.fa \
  -o GRCh38.bsbit \
  -t 8

Common options

Option	Argument	Default	Description
-r, --reference	FASTA path	Required	Plain, gzip, or BGZF reference genome FASTA used to build the index
-o, --output	Index path	Required	New path for the bsbit reference index
-t, --threads	Positive integer	1	Number of indexing workers

Reference requirements

Uncompressed FASTA is recommended for end-to-end workflows, although bsbit index can also read gzip- and BGZF-compressed FASTA. A .fai is not required for the command but is recommended to enable random access in bsbit call. Run the following command for your reference format:

Uncompressed FASTA:

samtools faidx GRCh38.fa

BGZF-compressed FASTA (creates both .fai and .gzi):

samtools faidx GRCh38.fa.gz

Ordinary gzip versus BGZF

If samtools faidx reports [E::fai_build3_core] Cannot index files compressed with gzip, please use bgzip, the FASTA is compressed with standard gzip, which does not support indexed random access. Although bsbit index can read the file sequentially, we recommend converting it to BGZF and generating its .fai and .gzi indexes before running bsbit index, so the same reference is ready for bsbit call:

gzip -cd downloaded-GRCh38.gz | bgzip -c > GRCh38.fa.gz
samtools faidx GRCh38.fa.gz

Index output

bsbit index writes the complete reference index at -o. Pass the same path to bsbit align -x. This index is used only for alignment; bsbit call reads the original FASTA directly.

Treat the bundle as one artifact; downstream commands do not modify it after generation. If the reference FASTA changes, rerun bsbit index to generate a new matching index before alignment.

Next

• Align reads
• Input data
• CLI reference