FragGeneScanRs: faster gene prediction for short reads [PDF]
BMC Bioinformatics, 2022 Background FragGeneScan is currently the most accurate and popular tool for gene prediction in short and error-prone reads, but its execution speed is insufficient for use on larger data sets.
Felix Van der Jeugt +2 more
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Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads [PDF]
Genome Biology, 2022 Background There is growing interest in retained introns in a variety of disease contexts including cancer and aging. Many software tools have been developed to detect retained introns from short RNA-seq reads, but reliable detection is complicated by ...
Julianne K. David +4 more
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High-resolution strain-level microbiome composition analysis from short reads [PDF]
Microbiome, 2023 Background Bacterial strains under the same species can exhibit different biological properties, making strain-level composition analysis an important step in understanding the dynamics of microbial communities.
Herui Liao, Yongxin Ji, Yanni Sun
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Targeted assembly of short sequence reads. [PDF]
PLoS ONE, 2011 As next-generation sequence (NGS) production continues to increase, analysis is becoming a significant bottleneck. However, in situations where information is required only for specific sequence variants, it is not necessary to assemble or align whole ...
René L Warren, Robert A Holt
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PMFFRC: a large-scale genomic short reads compression optimizer via memory modeling and redundant clustering [PDF]
BMC Bioinformatics, 2023 Background Genomic sequencing reads compressors are essential for balancing high-throughput sequencing short reads generation speed, large-scale genomic data sharing, and infrastructure storage expenditure.
Hui Sun +5 more
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Fast and accurate matching of cellular barcodes across short-reads and long-reads of single-cell RNA-seq experiments [PDF]
iScience, 2022 Summary: Single-cell RNA sequencing allows for characterizing the gene expression landscape at the cell type level. However, because of its use of short-reads, it is severely limited at detecting full-length features of transcripts such as alternative ...
Ghazal Ebrahimi +5 more
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Aligning Short Sequencing Reads with Bowtie [PDF]
Current Protocols in Bioinformatics, 2010 AbstractThis unit shows how to use the Bowtie package to align short sequencing reads, such as those output by second‐generation sequencing instruments. It also includes protocols for building a genome index and calling consensus sequences from Bowtie alignments using SAMtools. Curr. Protoc. Bioinform. 32:11.7.1‐11.7.14. © 2010 by John Wiley & Sons,
Benjamin Langmead
exaly +3 more sources
Short read sequence typing (SRST): multi-locus sequence types from short reads [PDF]
BMC Genomics, 2012 Background Multi-locus sequence typing (MLST) has become the gold standard for population analyses of bacterial pathogens. This method focuses on the sequences of a small number of loci (usually seven) to divide the population and is simple, robust and ...
Inouye Michael +3 more
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Instance-based error correction for short reads of disease-associated genes [PDF]
BMC Bioinformatics, 2021 Background Genomic reads from sequencing platforms contain random errors. Global correction algorithms have been developed, aiming to rectify all possible errors in the reads using generic genome-wide patterns.
Xuan Zhang +5 more
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Exploring high-quality microbial genomes by assembling short-reads with long-range connectivity [PDF]
Nature CommunicationsAlthough long-read sequencing enables the generation of complete genomes for unculturable microbes, its high cost limits the widespread adoption of long-read sequencing in large-scale metagenomic studies.
Zhenmiao Zhang +11 more
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