24 skills found
broadinstitute / PicardA set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
samtools / Hts SpecsSpecifications of SAM/BAM and related high-throughput sequencing file formats
HadoopGenomics / Hadoop BAMHadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework
cancerit / CaVEManSNV expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired (tumour/normal) cancer samples. Supports both bam and cram format via htslib
opencb / Genome MapsAn open-source high-performance web-based HTML5 genome browser. Genome Maps can be customized and allow browsing user data such as BAM and VCF files among other formats.
nf-core / BamtofastqConverts bam or cram files to fastq format and does quality control.
BioJulia / XAM.jlParse and process SAM and BAM formatted files
maragkakislab / SamqlSQL-like query language for the SAM/BAM file format
opencb-bigdata-viz / Genome MapsA new web-based HTML5 genome browser. Genome Maps can also browse BAM and VCFs files among other formats.
TimoLassmann / SamstatSAMStat displays various properties of next-generation sequencing reads stored in SAM/BAM format.
tobspr / Panda3D Bam ExporterBlender plugin to export to the .BAM format, used by Panda3D
MariaNattestad / CopycatCopycat is a simple script to capture and bin the read coverage across a genome from a bam file of read alignments. It relies on bedtools to get coverage for each individual nucleotide in the genome using bedtools genomecov, then bins and organizes these coverage values into 10kb bins and outputs the coverage information in a .csv format (for upload to SplitThreader) and in a .seg format (for viewing the copy number profile in IGV)
TuBieJun / MutViewMutView is a tool to look the reads cover a mutation in bam file, output file is html format, just like a lightweight IGV(Integrative Genomics Viewer).
AlexandrovLab / EnsembleVariantCallingPipelineThe EnsembleVariantCallingPipeline takes files in FASTQ or BAM format and performs SNV and INDEL variant calling from 4 variant callers (Mutect2, Strelka2, Varscan2, MuSE) and indel variant calling from 3 variant callers (Mutect2, Strelka2, Varscan2).
BioJulia / ReadDatastores.jlDatastores for reads, not your papa's FASTQ files.
Gerasimov94 / Tslint Bamboo FormatterNo description available
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voidberg / Eslint Bamboo FormatterA reporter for eslint which produces a report compatible with Atlassian Bamboo Mocha Test Parser.
zhaoshuoxp / ConvertersFormat Converters: bam2bigwig, FitHiC2bigInteract/longRange, HiCPro2JuiceBox, bedGrapgh2bigwig; GTF/BAM deduplicates
P3DCAT / BamUpgraderConverts old Panda3D BAM version 3.3 models to the new Panda3D BAM format.
