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BamTools: a C++ API and toolkit for analyzing and managing BAM files.
Bioinformatics. 2011 Jun 15;27(12):1691-2. doi: 10.1093/bioinformatics/btr174. Epub 2011 Apr 14.
2
SeqLib: a C ++ API for rapid BAM manipulation, sequence alignment and sequence assembly.
Bioinformatics. 2017 Mar 1;33(5):751-753. doi: 10.1093/bioinformatics/btw741.
3
BamToCov: an efficient toolkit for sequence coverage calculations.
Bioinformatics. 2022 Apr 28;38(9):2617-2618. doi: 10.1093/bioinformatics/btac125.
4
Poretools: a toolkit for analyzing nanopore sequence data.
Bioinformatics. 2014 Dec 1;30(23):3399-401. doi: 10.1093/bioinformatics/btu555. Epub 2014 Aug 20.
5
ppBAM: ProteinPaint BAM track for read alignment visualization and variant genotyping.
Bioinformatics. 2023 May 4;39(5). doi: 10.1093/bioinformatics/btad300.
6
SamQL: a structured query language and filtering tool for the SAM/BAM file format.
BMC Bioinformatics. 2021 Oct 2;22(1):474. doi: 10.1186/s12859-021-04390-3.
7
Alview: Portable Software for Viewing Sequence Reads in BAM Formatted Files.
Cancer Inform. 2015 Sep 13;14:105-7. doi: 10.4137/CIN.S26470. eCollection 2015.
8
Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets.
PLoS Comput Biol. 2018 Mar 28;14(3):e1006080. doi: 10.1371/journal.pcbi.1006080. eCollection 2018 Mar.
9
BEDTools: a flexible suite of utilities for comparing genomic features.
Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28.
10
cljam: a library for handling DNA sequence alignment/map (SAM) with parallel processing.
Source Code Biol Med. 2016 Aug 17;11:12. doi: 10.1186/s13029-016-0058-6. eCollection 2016.

引用本文的文献

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Population Genomics Reveals Panmixia in Pacific Sardine () of the North Pacific.
Evol Appl. 2025 Sep 4;18(9):e70154. doi: 10.1111/eva.70154. eCollection 2025 Sep.
2
A Prelude to Conservation Genomics: First Chromosome-Level Genome Assembly of a Flying Squirrel (Pteromyini: ).
Ecol Evol. 2025 Sep 1;15(9):e71905. doi: 10.1002/ece3.71905. eCollection 2025 Sep.
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Aquarius helicase facilitates HIV-1 integration into R-loop enriched genomic regions.
Nat Microbiol. 2025 Aug 20. doi: 10.1038/s41564-025-02089-2.
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The evolutionary dynamics of organellar pan-genomes in Arabidopsis thaliana.
Genome Biol. 2025 Aug 11;26(1):240. doi: 10.1186/s13059-025-03717-0.
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Allele frequency selection and no age-related increase in human oocyte mitochondrial mutations.
Sci Adv. 2025 Aug 8;11(32):eadw4954. doi: 10.1126/sciadv.adw4954. Epub 2025 Aug 6.
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SCoTCH-seq reveals that 5-hydroxymethylcytosine encodes regulatory information across DNA strands.
Proc Natl Acad Sci U S A. 2025 Aug 5;122(31):e2512204122. doi: 10.1073/pnas.2512204122. Epub 2025 Jul 31.
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Chromosome-level genome assembly of Sinocyclocheilus jii based on PacBio HiFi and Hi-C sequencing.
Sci Data. 2025 Jul 26;12(1):1303. doi: 10.1038/s41597-025-05663-9.

本文引用的文献

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A map of human genome variation from population-scale sequencing.
Nature. 2010 Oct 28;467(7319):1061-73. doi: 10.1038/nature09534.
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The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.
Genome Res. 2010 Sep;20(9):1297-303. doi: 10.1101/gr.107524.110. Epub 2010 Jul 19.
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BEDTools: a flexible suite of utilities for comparing genomic features.
Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28.
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The Sequence Alignment/Map format and SAMtools.
Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8.
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The human genome browser at UCSC.
Genome Res. 2002 Jun;12(6):996-1006. doi: 10.1101/gr.229102.

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