Legacy Reference Archives

Corrected transcription-strand references are distributed under the standard genome names. The archives distributed before those corrections are retained under _Legacy names so earlier analyses can be reproduced. Use the corrected name for new analyses; select a Legacy name only when comparing with results generated using the former reference.

Genome	Corrected reference/archive	Historical reference/archive
GRCh38	`GRCh38` / `GRCh38.tar.gz`	`GRCh38_Legacy` / `GRCh38_Legacy.tar.gz`
GRCh37	`GRCh37` / `GRCh37.tar.gz`	`GRCh37_Legacy` / `GRCh37_Legacy.tar.gz`
mm9	`mm9` / `mm9.tar.gz`	`mm9_Legacy` / `mm9_Legacy.tar.gz`
mm10	`mm10` / `mm10.tar.gz`	`mm10_Legacy` / `mm10_Legacy.tar.gz`
mm39	`mm39` / `mm39.tar.gz`	`mm39_Legacy` / `mm39_Legacy.tar.gz`
rn6	`rn6` / `rn6.tar.gz`	`rn6_Legacy` / `rn6_Legacy.tar.gz`
rn7	`rn7` / `rn7.tar.gz`	`rn7_Legacy` / `rn7_Legacy.tar.gz`
dog	`dog` / `dog.tar.gz`	`dog_Legacy` / `dog_Legacy.tar.gz`
c_elegans	`c_elegans` / `c_elegans.tar.gz`	`c_elegans_Legacy` / `c_elegans_Legacy.tar.gz`

Reproduce a Previous Analysis

Use a SigProfilerMatrixGenerator release that recognizes the _Legacy genome names. Install the Legacy reference, then select that same name when generating matrices. For example, if the previous analysis used the former GRCh38 archive:

SigProfilerMatrixGenerator install GRCh38_Legacy
SigProfilerMatrixGenerator matrix_generator previous_project GRCh38_Legacy /path/to/original_inputs

The equivalent Python calls are:

from SigProfilerMatrixGenerator import install as genInstall
from SigProfilerMatrixGenerator.scripts import SigProfilerMatrixGeneratorFunc as matGen

genInstall.install("GRCh38_Legacy")
matGen.SigProfilerMatrixGeneratorFunc(
    "previous_project", "GRCh38_Legacy", "/path/to/original_inputs"
)

Substitute the appropriate genome name from the table. An older reference installed under the standard name is not automatically renamed to its _Legacy identity after a software upgrade. Install and select the Legacy identity explicitly. If you also need the corrected reference for new analyses, install it under the standard name; the two identities can coexist.

Install from a Downloaded Archive

The archives are available at ftp://alexandrovlab-ftp.ucsd.edu/pub/tools/SigProfilerMatrixGenerator/. If automatic downloading is unavailable, download the exact archive filename from the table into a local directory, then pass the directory, not the archive path, to the CLI:

SigProfilerMatrixGenerator install GRCh38_Legacy --local_genome /path/to/archive-directory

For this example, the directory must contain GRCh38_Legacy.tar.gz. The CLI checks the installed chromosome files against the registered reference checksums. Do not rename a corrected archive to a Legacy filename or vice versa.

Reproducibility Limits

The Legacy archive preserves the previously distributed reference data, but does not restore an older version of the tool. For the closest possible reproduction, keep the original input files, SigProfilerMatrixGenerator and dependency versions, command arguments, and any BED/exome files. Differences caused by code or settings may remain even when the Legacy archive is used. Record the reference identity (GRCh38 versus GRCh38_Legacy) with each run.

The separate GRCh37_havana, GRCh38_havana, and mm10_havana references are not substitutes for these Legacy archives. See Reference Correctness for the scope of the corrections and Supported Genomes for genome descriptions.