@article{prjibelski_using_2020,
	title = {Using {SPAdes} De Novo Assembler},
	volume = {70},
	issn = {1934-3396, 1934-340X},
	url = {https://onlinelibrary.wiley.com/doi/10.1002/cpbi.102},
	doi = {10.1002/cpbi.102},
	number = {1},
	journaltitle = {Current Protocols in Bioinformatics},
	shortjournal = {Current Protocols in Bioinformatics},
	author = {Prjibelski, Andrey and Antipov, Dmitry and Meleshko, Dmitry and Lapidus, Alla and Korobeynikov, Anton},
	urldate = {2021-05-26},
	date = {2020-06},
	langid = {english},
}

@article{li_fast_2009,
	title = {Fast and accurate short read alignment with Burrows-Wheeler transform},
	volume = {25},
	issn = {1367-4811},
	doi = {10.1093/bioinformatics/btp324},
	abstract = {{MOTIVATION}: The enormous amount of short reads generated by the new {DNA} sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including {MAQ}, which is accurate, feature rich and fast enough to align short reads from a single individual. However, {MAQ} does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of {MAQ} is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals.
{RESULTS}: We implemented Burrows-Wheeler Alignment tool ({BWA}), a new read alignment package that is based on backward search with Burrows-Wheeler Transform ({BWT}), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. {BWA} supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from {AB} {SOLiD} machines. Evaluations on both simulated and real data suggest that {BWA} is approximately 10-20x faster than {MAQ}, while achieving similar accuracy. In addition, {BWA} outputs alignment in the new standard {SAM} (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source {SAMtools} software package.
{AVAILABILITY}: http://maq.sourceforge.net.},
	pages = {1754--1760},
	number = {14},
	journaltitle = {Bioinformatics (Oxford, England)},
	shortjournal = {Bioinformatics},
	author = {Li, Heng and Durbin, Richard},
	date = {2009-07-15},
	pmid = {19451168},
	pmcid = {PMC2705234},
	keywords = {Algorithms, Genomics, Sequence Alignment, Sequence Analysis, {DNA}, Software},
	file = {Full Text:/home/thomas/Zotero/storage/RAZYFYCS/Li and Durbin - 2009 - Fast and accurate short read alignment with Burrow.pdf:application/pdf},
}

@article{altschul_basic_1990,
	title = {Basic local alignment search tool},
	volume = {215},
	issn = {0022-2836},
	doi = {10.1016/S0022-2836(05)80360-2},
	abstract = {A new approach to rapid sequence comparison, basic local alignment search tool ({BLAST}), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair ({MSP}) score. Recent mathematical results on the stochastic properties of {MSP} scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward {DNA} and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long {DNA} sequences. In addition to its flexibility and tractability to mathematical analysis, {BLAST} is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.},
	pages = {403--410},
	number = {3},
	journaltitle = {Journal of Molecular Biology},
	shortjournal = {J Mol Biol},
	author = {Altschul, S. F. and Gish, W. and Miller, W. and Myers, E. W. and Lipman, D. J.},
	date = {1990-10-05},
	pmid = {2231712},
	keywords = {Algorithms, Software, Amino Acid Sequence, Base Sequence, Databases, Factual, Mutation, Sensitivity and Specificity, Sequence Homology, Nucleic Acid},
}

@article{quinlan_bedtools_2010,
	title = {{BEDTools}: a flexible suite of utilities for comparing genomic features},
	volume = {26},
	issn = {1460-2059, 1367-4803},
	url = {https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btq033},
	doi = {10.1093/bioinformatics/btq033},
	shorttitle = {{BEDTools}},
	pages = {841--842},
	number = {6},
	journaltitle = {Bioinformatics},
	author = {Quinlan, Aaron R. and Hall, Ira M.},
	urldate = {2021-05-26},
	date = {2010-03-15},
	langid = {english},
	file = {Full Text:/home/thomas/Zotero/storage/9QFL3W2J/Quinlan and Hall - 2010 - BEDTools a flexible suite of utilities for compar.pdf:application/pdf},
}

@article{chen_fastp_2018,
	title = {fastp: an ultra-fast all-in-one {FASTQ} preprocessor},
	volume = {34},
	issn = {1367-4803, 1460-2059},
	url = {https://academic.oup.com/bioinformatics/article/34/17/i884/5093234},
	doi = {10.1093/bioinformatics/bty560},
	shorttitle = {fastp},
	pages = {i884--i890},
	number = {17},
	journaltitle = {Bioinformatics},
	author = {Chen, Shifu and Zhou, Yanqing and Chen, Yaru and Gu, Jia},
	urldate = {2021-05-26},
	date = {2018-09-01},
	langid = {english},
	file = {Full Text:/home/thomas/Zotero/storage/6R62R2P4/Chen et al. - 2018 - fastp an ultra-fast all-in-one FASTQ preprocessor.pdf:application/pdf},
}

@article{faust_samblaster_2014,
	title = {{SAMBLASTER}: fast duplicate marking and structural variant read extraction},
	volume = {30},
	issn = {1367-4803, 1460-2059},
	url = {https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btu314},
	doi = {10.1093/bioinformatics/btu314},
	shorttitle = {{SAMBLASTER}},
	pages = {2503--2505},
	number = {17},
	journaltitle = {Bioinformatics},
	shortjournal = {Bioinformatics},
	author = {Faust, G. G. and Hall, I. M.},
	urldate = {2021-05-26},
	date = {2014-09-01},
	langid = {english},
	file = {Full Text:/home/thomas/Zotero/storage/5PRKXKZP/Faust and Hall - 2014 - SAMBLASTER fast duplicate marking and structural .pdf:application/pdf},
}