CUSHAW suite: parallel and efficient algorithms for NGS read alignment

DOI10.1007/978-3-319-59826-0_10MaRDI QIDQ3305533zbMATH OpenOpenAlexFDO

Authors Bertil Schmidt, Yongchao Liu

Publication date 7 August 2020

Published in Algorithms for Next-Generation Sequencing Data (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/978-3-319-59826-0_10

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Algorithms on strings (68W32)

Recommendations

• Comparison of BWA-MEM and NovoAlign using human whole-genome next-generation sequencing reads
• Comparative assessment of alignment algorithms for NGS data: features, considerations, implementations, and future
• G-MAPSEQ -- a new method for mapping reads to a reference genome
• String-matching and alignment algorithms for finding motifs in NGS data
• Algorithms for next-generation sequencing data. Techniques, approaches, and applications

Cites work

• Indexing compressed text
• Research in Computational Molecular Biology

Cited in

(5)

• Aligning flowgrams to DNA sequences
• Comparison of BWA-MEM and NovoAlign using human whole-genome next-generation sequencing reads
• SpliceTAPyR -- an efficient method for transcriptome alignment
• CUSHAW
• PSAEC: an improved algorithm for short read error correction using partial suffix arrays

Describes a project that uses

Uses Software

• ART
• BWA
• GASSST
• Bowtie 2
• PatternHunter
• BFAST
• ABySS
• Meta-IDBA
• SHRiMP
• SOAPdenovo
• Velvet
• Samtools
• GATK
• Soap

This page was built for publication: CUSHAW suite: parallel and efficient algorithms for NGS read alignment

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q3305533)