Commit f4b699e4 authored by mmassaviol's avatar mmassaviol
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Add citations

parent 117e94bd
citations: [
snakemake: [
"Köster, Johannes and Rahmann, Sven. Snakemake - A scalable bioinformatics workflow engine. Bioinformatics 2012."
],
multiqc: [
"Philip Ewels, Måns Magnusson, Sverker Lundin, Max Käller, MultiQC: summarize analysis results for multiple tools and samples in a single report, Bioinformatics, Volume 32, Issue 19, 1 October 2016, Pages 3047–3048, https://doi.org/10.1093/bioinformatics/btw354"
],
shiny: [
"Winston Chang, Joe Cheng, JJ Allaire, Yihui Xie and Jonathan McPherson (2019). shiny: Web Application Framework for R. https://CRAN.R-project.org/package=shiny"
]
]
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......@@ -61,4 +61,12 @@
"apt install -y openjdk-8-jre"
]
},
citations: [
picard_tools: [
"Picard Toolkit. 2019. Broad Institute, GitHub Repository. http://broadinstitute.github.io/picard/; Broad Institute"
],
samtools: [
"Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078–2079, https://doi.org/10.1093/bioinformatics/btp352"
]
]
}
......@@ -6,7 +6,7 @@
website: "https://samtools.github.io/bcftools/",
git: "https://github.com/samtools/bcftools",
documentation: "https://samtools.github.io/bcftools/howtos/index.html",
article: "",
article: "10.1093/bioinformatics/btr509",
multiqc: "bcftools",
commands:
[
......@@ -67,4 +67,12 @@
"apt install -y tabix"
}
},
citations: [
bcftools: [
"Heng Li, A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data, Bioinformatics, Volume 27, Issue 21, 1 November 2011, Pages 2987–2993, https://doi.org/10.1093/bioinformatics/btr509"
],
tabix: [
"Heng Li, Tabix: fast retrieval of sequence features from generic TAB-delimited files, Bioinformatics, Volume 27, Issue 5, 1 March 2011, Pages 718–719, https://doi.org/10.1093/bioinformatics/btq671"
]
]
}
{
id: blast_refseq,
name: blast refseq,
article: ~,
article: 10.1186/1471-2105-10-421,
website: "https://www.ncbi.nlm.nih.gov/genome/organelle/",
git: "",
description: "Blast fasta sequences on NCBI refseq mitochondrion database.",
......@@ -96,4 +96,9 @@
"python3 setup.py install"
]
},
citations: [
blast: [
"Camacho, C., Coulouris, G., Avagyan, V. et al. BLAST+: architecture and applications. BMC Bioinformatics 10, 421 (2009). https://doi.org/10.1186/1471-2105-10-421"
]
]
}
......@@ -182,4 +182,12 @@
"rm -r samtools-1.9 samtools-1.9.tar.bz2"
]
},
citations: [
bowtie: [
"Langmead, B., Trapnell, C., Pop, M. et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009). https://doi.org/10.1186/gb-2009-10-3-r25"
],
samtools: [
"Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078–2079, https://doi.org/10.1093/bioinformatics/btp352"
]
]
}
\ No newline at end of file
......@@ -134,4 +134,12 @@
"rm -r samtools-1.9 samtools-1.9.tar.bz2"
]
},
citations: [
bowtie2: [
"Langmead, B., Salzberg, S. Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357–359 (2012). https://doi.org/10.1038/nmeth.1923"
],
samtools: [
"Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078–2079, https://doi.org/10.1093/bioinformatics/btp352"
]
]
}
\ No newline at end of file
......@@ -108,4 +108,12 @@
"rm -r samtools-1.9 samtools-1.9.tar.bz2"
]
},
citations: [
bwa-mem2: [
"Vasimuddin Md, Sanchit Misra, Heng Li, Srinivas Aluru. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. IEEE Parallel and Distributed Processing Symposium (IPDPS), 2019"
],
samtools: [
"Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078–2079, https://doi.org/10.1093/bioinformatics/btp352"
]
]
}
\ No newline at end of file
......@@ -118,4 +118,15 @@
"rm -r samtools-1.9 samtools-1.9.tar.bz2"
]
},
citations: [
bwa: [
"Heng Li, Richard Durbin, Fast and accurate short read alignment with Burrows–Wheeler transform, Bioinformatics, Volume 25, Issue 14, 15 July 2009, Pages 1754–1760, https://doi.org/10.1093/bioinformatics/btp324"
],
bwa-mem: [
"Li H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997v1 [q-bio.GN]"
],
samtools: [
"Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078–2079, https://doi.org/10.1093/bioinformatics/btp352"
]
]
}
\ No newline at end of file
{
id: cstacks,
name: cstacks,
article: 10.1101/615385v1,
article: 10.1111/mec.15253,
website: "http://catchenlab.life.illinois.edu/stacks/comp/cstacks.php",
git: "",
description: "cstacks creates a set of consensus loci, merging alleles together.",
......@@ -63,5 +63,10 @@
"mv -t ../bin sstacks kmer_filter gstacks tsv2bam process_shortreads populations ustacks phasedstacks cstacks process_radtags",
"cd .. && rm -r stacks-2.5 stacks-2.5.tar.gz"
]
}
},
citations: [
stacks: [
" Rochette, NC, Rivera‐Colón, AG, Catchen, JM. Stacks 2: Analytical methods for paired‐end sequencing improve RADseq‐based population genomics. Mol Ecol. 2019; 28: 4737– 4754. https://doi.org/10.1111/mec.15253"
]
]
}
......@@ -127,5 +127,13 @@
pigz: [
"apt-get install -y pigz"
]
}
},
citations: [
cutadapt: [
"Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal, 17(1), pp. 10-12. doi:https://doi.org/10.14806/ej.17.1.200"
],
pigz: [
"Copyright(C) 2007-2017 MarkAdler <madler@alumni.caltech.edu>"
]
]
}
\ No newline at end of file
{
id: dada2,
name: dada2,
article: ~,
article: 10.1038/nmeth.3869,
website: "https://benjjneb.github.io/dada2",
git: "https://github.com/benjjneb/dada2",
description: "Fast and accurate sample inference from amplicon data with single-nucleotide resolution",
......@@ -173,5 +173,20 @@
name: taxonomy,
type: directory
}
],
citations: [
dada2: [
"Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13(7):581–583. doi:10.1038/nmeth.3869"
],
phyloseq: [
"McMurdie and Holmes (2013) phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data PLoS ONE 8(4):e61217"
],
biomformat: [
"Daniel McDonald, Jose C Clemente, Justin Kuczynski, Jai Ram Rideout, Jesse Stombaugh, Doug Wendel, Andreas Wilke, Susan Huse, John Hufnagle, Folker Meyer, Rob Knight, J Gregory Caporaso, The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome, GigaScience, Volume 1, Issue 1, December 2012, 2047–217X–1–7, https://doi.org/10.1186/2047-217X-1-7"
],
krona: [
"Ondov BD, Bergman NH, and Phillippy AM. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics. 2011 Sep 30; 12(1):385"
],
]
}
......@@ -141,4 +141,12 @@
"python3 setup.py install"
]
},
citations: [
deepvariant: [
"A universal SNP and small-indel variant caller using deep neural networks. Nature Biotechnology 36, 983–987 (2018). Ryan Poplin, Pi-Chuan Chang, David Alexander, Scott Schwartz, Thomas Colthurst, Alexander Ku, Dan Newburger, Jojo Dijamco, Nam Nguyen, Pegah T. Afshar, Sam S. Gross, Lizzie Dorfman, Cory Y. McLean, Mark A. DePristo, doi: https://doi.org/10.1038/nbt.4235"
],
samtools: [
"Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078–2079, https://doi.org/10.1093/bioinformatics/btp352"
]
]
}
\ No newline at end of file
......@@ -76,4 +76,18 @@
pheatmap: ['Rscript -e ''install.packages("pheatmap",Ncpus=8, clean=TRUE);library("pheatmap")''']
},
script: deseq2.script.R,
citations: [
DESeq2: [
"Love, M.I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15, 550 (2014). https://doi.org/10.1186/s13059-014-0550-8"
],
tximport: [
"Soneson C, Love MI, Robinson MD (2015). Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences. F1000Research, 4. doi: 10.12688/f1000research.7563.1"
],
GenomicFeatures: [
"Lawrence M, Huber W, Pagès H, Aboyoun P, Carlson M, et al. (2013) Software for Computing and Annotating Genomic Ranges. PLOS Computational Biology 9(8): e1003118. https://doi.org/10.1371/journal.pcbi.1003118"
],
pheatmap: [
"Kolde, R. (2012). Pheatmap: pretty heatmaps. R package version, 61, 617"
]
]
}
......@@ -81,4 +81,21 @@
pheatmap: ['Rscript -e ''install.packages("pheatmap",Ncpus=8, clean=TRUE);library("pheatmap"))''']
},
script: edger.script.R,
citations: [
edger: [
"Robinson MD, McCarthy DJ, Smyth GK (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26(1), 139-140. doi: 10.1093/bioinformatics/btp616"
],
limma: [
"Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Research, 43(7), e47. doi: 10.1093/nar/gkv007"
],
tximport: [
"Soneson C, Love MI, Robinson MD (2015). Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences. F1000Research, 4. doi: 10.12688/f1000research.7563.1"
],
GenomicFeatures: [
"Lawrence M, Huber W, Pagès H, Aboyoun P, Carlson M, et al. (2013) Software for Computing and Annotating Genomic Ranges. PLOS Computational Biology 9(8): e1003118. https://doi.org/10.1371/journal.pcbi.1003118"
],
pheatmap: [
"Kolde, R. (2012). Pheatmap: pretty heatmaps. R package version, 61, 617"
]
]
}
......@@ -176,4 +176,9 @@
"rm -r fastp-0.20.0 v0.20.0.tar.gz "
]
},
citations: [
fastp: [
"Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu, fastp: an ultra-fast all-in-one FASTQ preprocessor, Bioinformatics, Volume 34, Issue 17, 01 September 2018, Pages i884–i890, https://doi.org/10.1093/bioinformatics/bty560"
]
]
}
......@@ -44,4 +44,9 @@
install: {
fastqc: ["apt install -y fastqc=0.11.5+dfsg-6"]
},
citations: [
fastqc: [
"Andrews, S. (2010). FASTQC. A quality control tool for high throughput sequence data"
]
]
}
......@@ -37,4 +37,9 @@
"chmod +x freebayes",
],
},
citations: [
freebayes: [
"Garrison, E., & Marth, G. (2012). Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907."
]
]
}
......@@ -55,4 +55,9 @@
"apt install -y openjdk-8-jre"
]
},
citations: [
gatk: [
"McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., & DePristo, M. A. (2010). The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20(9), 1297‑1303. https://doi.org/10.1101/gr.107524.110 "
],
]
}
{
id: gatk_haplotype_caller,
name: GATK Haplotype Caller,
article: ~,
article: 10.1101/gr.107524.110,
website: "https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php",
git: "",
description: "The HaplotypeCaller is capable of calling SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region",
......@@ -69,4 +69,15 @@
"apt install -y openjdk-8-jre"
]
},
citations: [
gatk: [
"McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., & DePristo, M. A. (2010). The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20(9), 1297‑1303. https://doi.org/10.1101/gr.107524.110 "
],
bcftools: [
"Heng Li, A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data, Bioinformatics, Volume 27, Issue 21, 1 November 2011, Pages 2987–2993, https://doi.org/10.1093/bioinformatics/btr509"
],
samtools: [
"Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078–2079, https://doi.org/10.1093/bioinformatics/btp352"
]
]
}
......@@ -116,4 +116,9 @@
"rm -r genomescope-1.0.0 genomescope.tar.gz"
],
},
citations: [
genomescope: [
"Gregory W Vurture, Fritz J Sedlazeck, Maria Nattestad, Charles J Underwood, Han Fang, James Gurtowski, Michael C Schatz, GenomeScope: fast reference-free genome profiling from short reads, Bioinformatics, Volume 33, Issue 14, 15 July 2017, Pages 2202–2204, https://doi.org/10.1093/bioinformatics/btx153"
]
]
}
\ No newline at end of file
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