liqb's Stars
GitbookIO/gitbook
The open source frontend for GitBook doc sites
PHPOffice/PHPWord
A pure PHP library for reading and writing word processing documents
erikbrinkman/d3-dag
Layout algorithms for visualizing directed acyclic graphs
thieman/dagobah
Simple DAG-based job scheduler in Python
brentp/mosdepth
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
samtools/hts-specs
Specifications of SAM/BAM and related high-throughput sequencing file formats
etal/cnvkit
Copy number variant detection from targeted DNA sequencing
marcelm/cutadapt
Cutadapt removes adapter sequences from sequencing reads
biocommons/hgvs
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
abyzovlab/CNVnator
a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
exomiser/Exomiser
A Tool to Annotate and Prioritize Exome Variants
WGLab/InterVar
A bioinformatics software tool for clinical interpretation of genetic variants by the 2015 ACMG-AMP guideline
broadinstitute/ichorCNA
Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
imgag/ngs-bits
Short-read sequencing tools
antigenomics/vdjdb-db
🗂️ [vdjdb.cdr3.net is up and running] Git-based TCR database storage & management. Submissions welcome!
Illumina/canvas
Canvas - Copy number variant (CNV) calling from DNA sequencing data
ga4gh/task-execution-schemas
WGLab/phenolyzer
phenotype-based prioritization of candidate genes for human diseases
biocommons/uta
Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image
asher/chronos-python
python api for the chronos (for apache mesos) job scheduler
common-workflow-language/workflow-service
Implementation of the GA4GH Workflow Execution Service, a REST service for running workflows
qtop/qtop
qtop (pronounced queue-top) is a tool written in order to monitor the state of Queueing Systems, along with related information relevant on HPC & grid clusters. At present it supports **PBS, SGE & OAR** families. There is a historic reference for the prior shell version of the tool, at former CERN source:
EichlerLab/pacbio_variant_caller
SMRT-SV: Structural variant and indel caller for PacBio reads
rgcgithub/clamms
CLAMMS is a scalable tool for detecting common and rare copy number variants from whole-exome sequencing data.
MikeDacre/fyrd
Submit functions and shell scripts to torque and slurm clusters or local machines using python.
KCCG/seave
Seave is a web platform that enables genetic variants to be easily filtered and annotated with in silico pathogenicity prediction scores and annotations from popular disease databases. Seave stores genomic variation of all types and sizes, and allows filtering for specific inheritance patterns, quality values, allele frequencies and gene lists. Seave is open source and deployable locally, or on a cloud computing provider, and works readily with gene panel, exome and whole genome data, scaling from single labs to multi-institution scale.
umich-brcf-bioinf/Katana
Command-line tool to soft-clip reads based on primer locations.
weiyi-bitw/varnorm
ga4gh/hgvs-lib
C-based library for manipulating HGVS-formatted variants
jamescasbon/pygr
Python graph database framework for bioinformatics