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NF-Core / ViralRecon:NF-Core / ViralRecon V1.0.0 - 汞蝙蝠

Harshil Patel.; Sarai Varona.; SaraMonzón.; Jose Espinosa-Carrasco; Michael L Heuer.; Gisela Gabernet.; migueljulia.; 斯蒂芬凯利; 凯特林亚丁; Maxime Garcia.; jcurado


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    <subfield code="a">Sara Monzón</subfield>
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    <subfield code="a">Jose Espinosa-Carrasco</subfield>
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    <subfield code="u">UC Berkeley Amplab / Rise Lab</subfield>
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    <subfield code="a">Stephen Kelly</subfield>
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    <subfield code="a">Katrin Sameith</subfield>
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    <subfield code="u">@scilifelab | Karolinska Institutet.</subfield>
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    <subfield code="u">弗朗西斯克里克研究所</subfield>
    <subfield code="a">Harshil Patel</subfield>
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    <subfield code="a">NF-Core / ViralRecon:NF-Core / ViralRecon V1.0.0  - 汞蝙蝠</subfield>
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    <subfield code="a">&lt;p&gt;[1.0.0] - 2020-06-01&lt;/p&gt;

&lt;p&gt;Initial release of nf-core/viralrecon, created with the &lt;a href="http://nf-co.re"&gt;nf-core&lt;/a&gt; template.&lt;/p&gt;

&lt;p&gt;This pipeline is a re-implementation of the &lt;a href="//github.com/BU-ISCIII/SARS_Cov2_consensus-nf"&gt;SARS_Cov2_consensus-nf&lt;/a&gt; and &lt;a href="//github.com/BU-ISCIII/SARS_Cov2_assembly-nf"&gt;SARS_Cov2_assembly-nf&lt;/a&gt; pipelines initially developed by &lt;a href="//github.com/svarona"&gt;Sarai Varona&lt;/a&gt; and &lt;a href="//github.com/saramonzon"&gt;Sara Monzon&lt;/a&gt; from &lt;a href="//github.com/BU-ISCIII"&gt;BU-ISCIII&lt;/a&gt;. Porting both of these pipelines to nf-core was an international collaboration between numerous contributors and developers, led by &lt;a href="//github.com/drpatelh"&gt;Harshil Patel&lt;/a&gt; from the &lt;a href="//www.crick.ac.uk/research/science-technology-platforms/bioinformatics-and-biostatistics/"&gt;The Bioinformatics &amp;amp; Biostatistics Group&lt;/a&gt; at &lt;a href="//www.crick.ac.uk/"&gt;弗朗西斯克里克研究所&lt;/a&gt;, London. We appreciated the need to have a portable, reproducible and scalable pipeline for the analysis of COVID-19 sequencing samples and so the Avengers Assembled!&lt;/p&gt;

&lt;p&gt;Pipeline summary&lt;/p&gt;

&lt;ol&gt;
	&lt;li&gt;Download samples via SRA, ENA or GEO ids (&lt;a href="//ena-docs.readthedocs.io/en/latest/retrieval/file-download.html"&gt;&lt;code&gt;ENA FTP&lt;/code&gt;&lt;/a&gt;, &lt;a href="//github.com/rvalieris/parallel-fastq-dump"&gt;&lt;code&gt;parallel-fastq-dump&lt;/code&gt;&lt;/a&gt;; &lt;em&gt;if required&lt;/em&gt;)&lt;/li&gt;
	&lt;li&gt;Merge re-sequenced FastQ files (&lt;a href="http://www.linfo.org/cat.html"&gt;&lt;code&gt;cat&lt;/code&gt;&lt;/a&gt;; &lt;em&gt;if required&lt;/em&gt;)&lt;/li&gt;
	&lt;li&gt;Read QC (&lt;a href="//www.bioinformatics.babraham.ac.uk/projects/fastqc/"&gt;&lt;code&gt;FastQC&lt;/code&gt;&lt;/a&gt;)&lt;/li&gt;
	&lt;li&gt;Adapter trimming (&lt;a href="//github.com/OpenGene/fastp"&gt;&lt;code&gt;fastp&lt;/code&gt;&lt;/a&gt;)&lt;/li&gt;
	&lt;li&gt;Variant calling
	&lt;ol&gt;
		&lt;li&gt;Read alignment (&lt;a href="http://bowtie-bio.sourceforge.net/bowtie2/index.shtml"&gt;&lt;code&gt;Bowtie 2&lt;/code&gt;&lt;/a&gt;)&lt;/li&gt;
		&lt;li&gt;Sort and index alignments (&lt;a href="//sourceforge.net/projects/samtools/files/samtools/"&gt;&lt;code&gt;SAMtools&lt;/code&gt;&lt;/a&gt;)&lt;/li&gt;
		&lt;li&gt;Primer sequence removal (&lt;a href="//github.com/andersen-lab/ivar"&gt;&lt;code&gt;iVar&lt;/code&gt;&lt;/a&gt;; &lt;em&gt;amplicon data only&lt;/em&gt;)&lt;/li&gt;
		&lt;li&gt;Duplicate read marking (&lt;a href="//broadinstitute.github.io/picard/"&gt;&lt;code&gt;picard&lt;/code&gt;&lt;/a&gt;; &lt;em&gt;removal optional&lt;/em&gt;)&lt;/li&gt;
		&lt;li&gt;Alignment-level QC (&lt;a href="//broadinstitute.github.io/picard/"&gt;&lt;code&gt;picard&lt;/code&gt;&lt;/a&gt;, &lt;a href="//sourceforge.net/projects/samtools/files/samtools/"&gt;&lt;code&gt;SAMtools&lt;/code&gt;&lt;/a&gt;)&lt;/li&gt;
		&lt;li&gt;Choice of multiple variant calling and consensus sequence generation routes (&lt;a href="http://dkoboldt.github.io/varscan/"&gt;&lt;code&gt;VarScan 2&lt;/code&gt;&lt;/a&gt;, &lt;a href="http://samtools.github.io/bcftools/bcftools.html"&gt;&lt;code&gt;BCFTools&lt;/code&gt;&lt;/a&gt;, &lt;a href="//github.com/arq5x/bedtools2/"&gt;&lt;code&gt;BEDTools&lt;/code&gt;&lt;/a&gt; &lt;em&gt;||&lt;/em&gt; &lt;a href="//github.com/andersen-lab/ivar"&gt;&lt;code&gt;iVar variants and consensus&lt;/code&gt;&lt;/a&gt; &lt;em&gt;||&lt;/em&gt; &lt;a href="http://samtools.github.io/bcftools/bcftools.html"&gt;&lt;code&gt;BCFTools&lt;/code&gt;&lt;/a&gt;, &lt;a href="//github.com/arq5x/bedtools2/"&gt;&lt;code&gt;BEDTools&lt;/code&gt;&lt;/a&gt;)
		&lt;ul&gt;
			&lt;li&gt;Variant annotation (&lt;a href="http://snpeff.sourceforge.net/SnpEff.html"&gt;&lt;code&gt;SnpEff&lt;/code&gt;&lt;/a&gt;, &lt;a href="http://snpeff.sourceforge.net/SnpSift.html"&gt;&lt;code&gt;SnpSift&lt;/code&gt;&lt;/a&gt;)&lt;/li&gt;
			&lt;li&gt;Consensus assessment report (&lt;a href="http://quast.sourceforge.net/quast"&gt;&lt;code&gt;QUAST&lt;/code&gt;&lt;/a&gt;)&lt;/li&gt;
		&lt;/ul&gt;
		&lt;/li&gt;
	&lt;/ol&gt;
	&lt;/li&gt;
	&lt;li&gt;&lt;em&gt;De novo&lt;/em&gt; assembly
	&lt;ol&gt;
		&lt;li&gt;Primer trimming (&lt;a href="//cutadapt.readthedocs.io/en/stable/guide.html"&gt;&lt;code&gt;Cutadapt&lt;/code&gt;&lt;/a&gt;; &lt;em&gt;amplicon data only&lt;/em&gt;)&lt;/li&gt;
		&lt;li&gt;Removal of host reads (&lt;a href="http://ccb.jhu.edu/software/kraken2/"&gt;&lt;code&gt;Kraken 2&lt;/code&gt;&lt;/a&gt;)&lt;/li&gt;
		&lt;li&gt;Choice of multiple assembly tools (&lt;a href="http://cab.spbu.ru/software/spades/"&gt;&lt;code&gt;SPAdes&lt;/code&gt;&lt;/a&gt; &lt;em&gt;||&lt;/em&gt; &lt;a href="http://cab.spbu.ru/software/meta-spades/"&gt;&lt;code&gt;metaSPAdes&lt;/code&gt;&lt;/a&gt; &lt;em&gt;||&lt;/em&gt; &lt;a href="//github.com/rrwick/Unicycler"&gt;&lt;code&gt;Unicycler&lt;/code&gt;&lt;/a&gt; &lt;em&gt;||&lt;/em&gt; &lt;a href="//github.com/GATB/minia"&gt;&lt;code&gt;minia&lt;/code&gt;&lt;/a&gt;)
		&lt;ul&gt;
			&lt;li&gt;Blast to reference genome (&lt;a href="//blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch"&gt;&lt;code&gt;blastn&lt;/code&gt;&lt;/a&gt;)&lt;/li&gt;
			&lt;li&gt;Contiguate assembly (&lt;a href="//www.sanger.ac.uk/science/tools/pagit"&gt;&lt;code&gt;ABACAS&lt;/code&gt;&lt;/a&gt;)&lt;/li&gt;
			&lt;li&gt;Assembly report (&lt;a href="//github.com/BU-ISCIII/plasmidID"&gt;&lt;code&gt;PlasmidID&lt;/code&gt;&lt;/a&gt;)&lt;/li&gt;
			&lt;li&gt;Assembly assessment report (&lt;a href="http://quast.sourceforge.net/quast"&gt;&lt;code&gt;QUAST&lt;/code&gt;&lt;/a&gt;)&lt;/li&gt;
			&lt;li&gt;Call variants relative to reference (&lt;a href="//github.com/lh3/minimap2"&gt;&lt;code&gt;Minimap2&lt;/code&gt;&lt;/a&gt;, &lt;a href="//github.com/ekg/seqwish"&gt;&lt;code&gt;seqwish&lt;/code&gt;&lt;/a&gt;, &lt;a href="//github.com/vgteam/vg"&gt;&lt;code&gt;vg&lt;/code&gt;&lt;/a&gt;, &lt;a href="//github.com/rrwick/Bandage"&gt;&lt;code&gt;Bandage&lt;/code&gt;&lt;/a&gt;)&lt;/li&gt;
			&lt;li&gt;Variant annotation (&lt;a href="http://snpeff.sourceforge.net/SnpEff.html"&gt;&lt;code&gt;SnpEff&lt;/code&gt;&lt;/a&gt;, &lt;a href="http://snpeff.sourceforge.net/SnpSift.html"&gt;&lt;code&gt;SnpSift&lt;/code&gt;&lt;/a&gt;)&lt;/li&gt;
		&lt;/ul&gt;
		&lt;/li&gt;
	&lt;/ol&gt;
	&lt;/li&gt;
	&lt;li&gt;Present QC and visualisation for raw read, alignment, assembly and variant calling results (&lt;a href="http://multiqc.info/"&gt;&lt;code&gt;MultiQC&lt;/code&gt;&lt;/a&gt;)&lt;/li&gt;
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