Chez Charles/ tags/ pages tagged software
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Muscle5: High-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny.
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Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data.
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Goel M, Sun H, Jiao WB, Schneeberger K. SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies.
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Minimally-overlapping words for sequence similarity search.
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CNEr: A toolkit for exploring extreme noncoding conservation.
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AnchorWave: Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism, and whole-genome duplication.
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Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes.
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BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes.
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Identifying and removing haplotypic duplication in primary genome assemblies.
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Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes.
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SBML Level 3: an extensible format for the exchange and reuse of biological models.
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Accurate identification of centromere locations in yeast genomes using Hi-C.
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D-GENIES: dot plot large genomes in an interactive, efficient and simple way.
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Predicting Genes in Single Genomes with AUGUSTUS.
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BUSCO: Assessing Genome Assembly and Annotation Completeness.
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RaGOO: fast and accurate reference-guided scaffolding of draft genomes.
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Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies.
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FACIL: Fast and Accurate Genetic Code Inference and Logo.
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Using data-compressors for statistical analysis of problems on homogeneity testing and classification
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Inferring whole-genome histories in large population datasets.
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Fast and accurate de novo genome assembly from long uncorrected reads.
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Mapping and phasing of structural variation in patient genomes using nanopore sequencing.
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Scaffolding of long read assemblies using long range contact information.
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Ragout-a reference-assisted assembly tool for bacterial genomes.
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Chromosome assembly of large and complex genomes using multiple references.
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plyranges: a grammar of genomic data transformation.
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NanoPARE: parallel analysis of RNA 5' ends from low-input RNA.
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ZIFA: Dimensionality reduction for zero-inflated single-cell gene expression analysis.
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NanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sites.
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Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures.
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biobambam: tools for read pair collation based algorithms on BAM files
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Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms.
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Profiling model T-cell metagenomes with short reads.
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The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants.
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