Evidence map›Paper›PMID 40964079›Full record

ArticleArXiv2025

Finding low-complexity DNA sequences with longdust.

Heng Li, Brian Li

Abstract readPreprint
PubMed Full text at PMC
In one paragraph

Article in ArXiv, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

2 authors.

Heng LiDepartment of Biomedical Informatics, Harvard Medical School, 10 Shattuck St, Boston, MA 02215, USA.ORCID 0000-0003-4874-2874
Brian LiCommonwealth School, Boston, MA 02116, USA.

Funding

The WashU-UCSC-EBI Human Genome Reference Center."U41HG010972 · NHGRI · WASHINGTON UNIVERSITY · PI Ting Wang · 2019 to 2026
$24.9M
Advanced computational methods in analyzing high-throughput sequencing dataR01HG010040 · NHGRI · DANA-FARBER CANCER INST · PI Heng Li · 2018 to 2026
$3.7M
Enhancement and further development of informatics methods for long-read cancer sequencingU24CA294203 · NCI · DANA-FARBER CANCER INST · PI Catarina D. Campbell, Heng Li · 2024 to 2026
$2.6M
Tools for comprehensive variant characterization using the pangenomeU01HG013748 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI LI, HENG, MARSCHALL, TOBIAS · 2024 to 2024
$1.7M
Calling germline and mosaic variants from long genomic and RNA-seq readsR01HG014175 · NHGRI · DANA-FARBER CANCER INST · PI Heng Li · 2025 to 2026
$1.0M
NCI NIH HHS U24 CA294203NHGRI NIH HHS R01 HG010040NHGRI NIH HHS R01 HG014175NHGRI NIH HHS U01 HG013748NHGRI NIH HHS U41 HG010972
6 · The paper itself

Abstract

Motivation: Low-complexity (LC) DNA sequences are compositionally repetitive sequences that are often associated with spurious homologous matches and variant calling artifacts. While algorithms for identifying LC sequences exist, they either do not define complexity mathematically or are inefficient with long or variable context windows. Results: Longdust is a new algorithm that efficiently identifies long LC sequences including centromeric satellite and tandem repeats with moderately long motifs. It defines string complexity by statistically modeling the Availability and implementation: https://github.com/lh3/longdust.

Identifiers

PMID40964079
PMCPMC12440070

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.