khmer discussions¶

2014-what-is-khmer.rst 2013-khmer-counting-paper.rst 2014-estimate-genome-size-shotgun.rst 2014-assembling-soil.rst 2014-downsample-to-given-coverage.rst 2014-estimate-sequencing-saturation.rst 2014-estimate-total-genome-size.rst 2014-how-good-is-megahit.rst 2014-more-on-khmer-counting.rst 2014-response-to-reviewers-khmer-counting.rst 2014-slice-reads-by-coverage.rst 2015-a-generator-api-for-khmer.rst 2015-khmer-impact.rst 2015-semi-streaming-paper.rst 2015-wok-counting.rst 2015-wok-error-correction.rst 2015-wok-evaluate.rst 2015-wok-labelhash.rst 2015-wok-notes.rst 2015-wok-variant-calling.rst 2016-partitioning-no-more.rst an-assembly-handbook-for-khmer.rst announcing-khmer-protocols.rst asmw12.rst diginorm-paper-posted.rst trinity-in-silico-normalize.rst the-future-of-bioinformatics-part-1a.rst the-future-of-bioinformatics-part-1b.rst the-future-of-khmer-2013-version.rst releasing-khmer-1_0.rst multithreaded-read-parsing-in-khmer.rst khmer-counting-reviews.rst kmer-counting-benchmarks.rst kmer-filtering.rst kmer-percolation-published.rst error-detection-for-metagenome-and-mrnaseq.rst diginorm-paper-posted.rst

Background (data structures and algorithms)¶

2013-pycon-awesome-big-data-algorithms-talk.rst 2015-jclub-bloom-filter-trie.rst 2015-review-bloomtree.rst 2015-sequence-bloom-trees-thoughts.rst assembly-part-i.rst beachcombers-dilemma.rst

sourmash¶

2016-sourmash.rst

Software development¶

2014-being-release-manager-khmer.rst 2014-research-coding.rst 2015-growing-sustainable-software-development-process.rst 2015-how-should-we-think-about-research-software.rst 2015-how-we-develop-software.rst 2015-authorship-on-software-papers.rst 2015-modifying-our-dev-process.rst 2015-more-on-software.rst 2015-on-benchmarking.rst 2015-on-licensing-in-bioinformatics.rst 2015-on-sustainable-scientific-software.rst 2015-software-as-a-primary-product-of-science.rst 2016-sustaining-research-software-development.rst automated-testing-and-research-software.rst software-testing-in-science.rst software-maintenance-grant.rst software-quality-death-spiral.rst software-sucks-montage-1.rst research-software-quality-a-rant.rst research-software-reuse.rst on-code-review-of-scientific-code.rst

Social and cultural experiments¶

2014-citations.rst 2014-khmer-hackathon.rst 2014-our-paper-process.rst 2015-another-khmer-sprint.rst 2015-bioinformatics-middle-class.rst crowdsourced-analysis-with-data-privacy-sunset.rst crowdsourcing-my-research.rst blog-practicing-open-science.rst replication-i.rst openness-and-online-reputation-recognized-in-grant-reviews.rst open-transcriptome-project-thoughts.rst ladder-of-academic-software-notsuck.rst

2014-loligo-transcriptome-data.rst

Dunno:

2014-pycon.rst 2014-scalable-cms-problems.rst 2015-response-to-software-myths.rst

assessing-impact-of-openness.rst

building-better-metagenomics-pipelines.rst cognitive-dissonance.rst error-detection-for-metagenome-and-mrnaseq.rst haemonchus-my-story.rst how-do-errors-modify-dbg-connectivity.rst how-much-sequencing-is-needed.rst illumina-read-phenomenology.rst jgr-assembling-the-amazon.rst khmer-counting-reviews.rst kmer-counting-benchmarks.rst kmer-filtering.rst kmer-percolation-published.rst multithreaded-read-parsing-in-khmer.rst ngs-2012-course.rst notes-for-panel-on-reviewing.rst open-transcriptome-project-thoughts.rst openness-and-risk-benefit.rst publishing-paper-pipelines.rst releasing-khmer-1_0.rst replication-i.rst the-future-of-khmer-2013-version.rst trinity-in-silico-normalize.rst trying-out-cram.rst why-you-shouldnt-use-diginorm.rst 2012-scripps-swc-postmortem.rst 2013-a5-paper-review.rst 2013-assemblathon-review-i.rst 2013-assembly-masterclass.rst 2013-dsk-review.rst 2013-gbmf-mmi.rst 2013-how-can-we-help.rst 2013-khmer-counting-paper.rst 2013-pycon-awesome-big-data-algorithms-talk.rst 2013-ray-meta-review.rst 2013-review-troubling-trends.rst 2013-seattle-bootcamp.rst 2013-sesync-meeting.rst 2013-swc-arizona.rst 2013-teaching-workshops.rst 2014-another-email-interview.rst 2014-being-release-manager-khmer.rst 2014-bosc-keynote.rst 2014-citations.rst 2014-containers.rst 2014-davis-and-training.rst 2014-davis-swc-training.rst 2014-eli-conversation.rst 2014-estimate-genome-size-shotgun.rst 2014-estimate-sequencing-saturation.rst 2014-estimate-total-genome-size.rst 2014-fifth-angus.rst 2014-how-good-is-megahit.rst 2014-imagine.rst 2014-khmer-hackathon.rst 2014-mhacks-hackathon.rst 2014-moore-ddd-award.rst 2014-moore-ddd-round2-final.rst 2014-moore-ddd-round2.rst 2014-moore-ddd-stmt-of-work.rst 2014-moore-ddd-talk.rst 2014-myths-of-computational-reproducibility.rst 2014-nih-adds-training-breakout.rst 2014-nih-adds-up-meeting.rst 2014-on-cami.rst 2014-open-and-tenured.rst 2014-our-paper-process.rst 2014-plans-for-davis.rst 2014-pycon.rst 2014-response-to-reviewers-khmer-counting.rst 2014-swc-toronto-training.rst 2014-teaching-undergrads-with-github.rst 2014-the-emerging-field-of-data-intensive-biology.rst 2014-what-is-khmer.rst 2015-a-generator-api-for-khmer.rst 2015-another-khmer-sprint.rst 2015-authorship-on-software-papers.rst 2015-bioinformatics-middle-class.rst 2015-cyberinfrastructure-sust.rst 2015-davis-swc.rst 2015-docker-and-replicating-papers.rst 2015-eigengenome-review.rst 2015-growing-sustainable-software-development-process.rst 2015-how-should-we-think-about-research-software.rst 2015-how-we-develop-software.rst 2015-jclub-etc-on-reproducibility.rst 2015-khmer-impact.rst 2015-megahit-review.rst 2015-modifying-our-dev-process.rst 2015-more-on-software.rst 2015-nih-tcc-draft.rst 2015-on-benchmarking.rst 2015-on-licensing-in-bioinformatics.rst 2015-on-sustainable-scientific-software.rst 2015-osf-galaxy-dibs-funding.rst 2015-osos-meeting.rst 2015-pycon-ally-workshop.rst 2015-response-to-software-myths.rst 2015-review-bloomtree.rst 2015-sequence-bloom-trees-thoughts.rst 2015-small-batch.rst 2015-software-as-a-primary-product-of-science.rst 2015-software-carpentry-affiliate.rst 2015-software-hardening-q.rst 2015-some-workshop-or-unconference-ideas.rst 2015-transcriptomes-with-docker.rst 2015-using-hypothesis-on-workshop-sites.rst 2015-we-live-in-a-bubble.rst 2015-what-should-I-teach-about-Jupyter.rst 2015-wok-counting.rst 2015-wok-error-correction.rst 2015-wok-notes.rst 2016-containerization-disaster.rst 2016-docker-at-bids.rst 2016-mybinder-workshop-proposal.rst 2016-mybinder.rst 2016-on-pppr.rst 2016-sbg-patent-email.rst 2016-sourmash.rst 2016-sustaining-research-software-development.rst 2016-teaching-code-review.rst advice-on-academic-OSS.rst aggressive-competence.rst anecdotal-science.rst announcing-khmer-protocols.rst asmw12.rst assemblathon-and-assembly.rst automated-testing-and-research-software.rst avoid-time-wasting-morons.rst better-oss-unpaid.rst big-data-biology-2.rst big-data-biology.rst bio-ci-needs.rst bioinformatics-training-suites.rst blog-practicing-open-science.rst blog-review-criteria-for-bioinfo.rst

building-better-metagenomics-pipelines.rst

cloud-not-the-solution.rst

cognitive-dissonance.rst

computation-for-terabase-metagenomics.rst

data-intensive-science-and-workflows.rst

data-management.rst

four-reasons-i-wont-use-your-data-analysis-pipeline.rst

google-filter.rst grants-posted.rst

integrating-the-academic-and-open-source.rst

jgi-workshop.rst

life-science-software.rst

msu-position.rst necessity-vs-sufficiency.rst new-to-python-projects.rst nextgen-sequencing-proposal.rst

not-sucking-v2.rst not-sucking.rst ohio-and-beyond.rst on-academia.rst

principles-of-computational-science.rst

publishing-paper-pipelines.rst

reject-software-engineering.rst

science-and-open-science.rst

sequence-squeezing.rst software-is-hard-link.rst software-licensing.rst the-challenges-of-mrnaseq-analysis.rst the-cost-of-open-science.rst whack-a-mole.rst whats-in-it-for-me.rst why-you-shouldnt-use-diginorm.rst