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Papers #10

2 of 19 tasks
thejmazz opened this issue May 27, 2016 · 2 comments
2 of 19 tasks

Papers #10

thejmazz opened this issue May 27, 2016 · 2 comments


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thejmazz commented May 27, 2016

Not all are directly relevant, this has become somewhat of a reading list for myself.

  • Sequence Alignment/Map Format Specification
  • The Sequence Alignment/Map format and SAMtools
  • Trimmomatic- a flexible trimmer for Illumina sequence data
  • The khmer software package- enabling efficient nucleotide sequence analysis
  • Disk-based k-mer counting on a PC
  • Teaser- Individualized benchmarking and optimization of read mapping results for NGS data
  • KMC 2- Fast and resource-frugal k-mer counting
  • Snakemake—a scalable bioinformatics workflow engine
  • Nextflowposterver3
  • Rust-Bio- a fast and safe bioinformatics library
  • Differentially expressed genes associated with adaptation to different thermal environments in three sympatric Cuban Anolis lizards
  • NextflowWorkbench: Reproducible and Reusable Workflows for Beginners and Experts.
  • Comparison of normalization and differential expression analyses using RNA-Seq data from 726 individual Drosophila melanogaster
  • A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis
  • near-optimal probabilistic rna-seq quantification - snakemake pipeline in repo - see this
  • BioDB extractor: customized data extraction system for commonly used bioinformatics databases
  • Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome
  • The Lair: A resource for exploratory analysis of published RNA-Seq data
  • The gene cortex controls mimicry and crypsis in butterflies and moths
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Maybe this should be moved to bionode-watermill repo or closed if not relevant anymore.

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this was mostly just my reading list for things related to gsoc project. ill close

@bmpvieira bmpvieira moved this from Backlog to Done in Bionode Project Board Mar 29, 2017
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