benchmarking
cancer
climate-change
clojure
cloudbiolinux
docker
galaxy
germline
- Validated variant calling with human genome build 38
- Validating generalized incremental joint variant calling with GATK HaplotypeCaller, FreeBayes, Platypus and samtools
- Validated whole genome structural variation detection using multiple callers
- Updated comparison of variant detection methods: Ensemble, FreeBayes and minimal BAM preparation pipelines
- Framework for evaluating variant detection methods: comparison of aligners and callers
- The influence of reduced resolution quality scores on alignment and variant calling
- An automated ensemble method for combining and evaluating genomic variants from multiple callers
- Genomics X Prize public phase update: variant classification and de novo calling
- Genomics X Prize public phase: reference genome preparation and comparisons to Illumina and Complete Genomics
how-to
- Extending the GATK for custom variant comparisons using Clojure
- Summarizing next-gen sequencing variation statistics with Hadoop using Cascalog
- Automated retrieval of expression data with Python and R
- Gene Ontology analysis with Python and Bioconductor
- Differential expression analysis with Bioconductor and Python
- Trimming adaptors from short read sequences
- Sorting genomic alignments using Python
- Finding and displaying short reads clustered in the genome
- Examining and adjusting your GFF file
- More python GFF parsing -- iterative parsing and GFF2 nested features
- Python GFF parser update -- parallel parsing and GFF2
- MapReduce implementation of GFF parsing for Biopython
- Exploring BioPerl GenBank to GFF mapping
- Organization of literature using PubMed related articles
- Automated protein conservation display from BLAST alignments
- Location and duplication information from Ensembl
- Graphing of variables before classification
- Finding proteins with related function using semantic clustering
- Extracting protein characteristics for an InterPro domain
- Extracting keywords from biological text using Zemanta
- Comparative genomics information retrieval from Ensembl
- Parsing GoPubMed RDF with Sparta
- Standard Ontologies in BioSQL
infrastructure
- Benchmarking variation and RNA-seq analyses on Amazon Web Services with Docker
- Improving reproducibility and installation of genomic analysis pipelines with Docker
- Scaling variant detection pipelines for whole genome sequencing analysis
- Making next-generation sequencing analysis pipelines easier with BioCloudCentral and Galaxy integration
- Parallel approaches in next-generation sequencing analysis pipelines
- Distributed exome analysis pipeline with CloudBioLinux and CloudMan
- Parallel upload to Amazon S3 with python, boto and multiprocessing
- Next generation sequencing information management and analysis system for Galaxy
- CloudBioLinux: progress on bioinformatics cloud images and data
- Automated build environment for Bioinformatics cloud images
- Usage plans for Amazon Web Services research grant
- Evaluating key-value and document stores for short read data
- BioSQL on Google App Engine
- Authorization schema for BioSQL databases
jobs
joint-calling
lims
open-source
- Summary from Bioinformatics Open Science Codefest 2013: Tools, infrastructure, standards and visualization
- Bioinformatics open source interoperability Hackathon at the Broad Institute
- CloudBioLinux: progress on bioinformatics cloud images and data
- Automated build environment for Bioinformatics cloud images
- Biopython projects for Google Summer of Code 2010
- Python query interface to BioGateway SPARQL endpoint and InterMine
- Thoughts from BOSC 2009; Python in bioinformatics
- Talking at BOSC 2009 about publishing biological data on the web
- Biopython projects for Google Summer of Code
- Initial GFF parser for Biopython
rna-seq
small-rna
small-variants
- Developing low frequency filters for cancer variant calling using VarDict
- Validated variant calling with human genome build 38
- Validating multiple cancer variant callers and prioritization in tumor-only samples
- Benchmarking variation and RNA-seq analyses on Amazon Web Services with Docker
- Validating generalized incremental joint variant calling with GATK HaplotypeCaller, FreeBayes, Platypus and samtools
- Whole genome trio variant calling evaluation: low complexity regions, GATK VQSR and high depth filters
- Improving reproducibility and installation of genomic analysis pipelines with Docker
- Updated comparison of variant detection methods: Ensemble, FreeBayes and minimal BAM preparation pipelines
- Scaling variant detection pipelines for whole genome sequencing analysis
- Framework for evaluating variant detection methods: comparison of aligners and callers
- The influence of reduced resolution quality scores on alignment and variant calling
- An automated ensemble method for combining and evaluating genomic variants from multiple callers
- Genomics X Prize public phase update: variant classification and de novo calling
- Genomics X Prize public phase: reference genome preparation and comparisons to Illumina and Complete Genomics
structural-variation
synthetic-biology
validation
- Developing low frequency filters for cancer variant calling using VarDict
- Validating small RNA analysis with miRQC
- Validated variant calling with human genome build 38
- Validating multiple cancer variant callers and prioritization in tumor-only samples
- Validating generalized incremental joint variant calling with GATK HaplotypeCaller, FreeBayes, Platypus and samtools
- Validated whole genome structural variation detection using multiple callers
- Whole genome trio variant calling evaluation: low complexity regions, GATK VQSR and high depth filters
- Updated comparison of variant detection methods: Ensemble, FreeBayes and minimal BAM preparation pipelines
- Framework for evaluating variant detection methods: comparison of aligners and callers
- The influence of reduced resolution quality scores on alignment and variant calling
- An automated ensemble method for combining and evaluating genomic variants from multiple callers
- Genomics X Prize public phase update: variant classification and de novo calling
- Genomics X Prize public phase: reference genome preparation and comparisons to Illumina and Complete Genomics
visualization
xprize