Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
Projects in Awesome Lists by edawson
A curated list of projects in awesome lists by edawson .
https://github.com/edawson/gfakluge
A C++ library and utilities for manipulating the Graphical Fragment Assembly format.
genomics gfa graph-representation parsing
Last synced: 10 Nov 2024
https://github.com/edawson/rkmh
Classify sequencing reads using MinHash.
bioinformatics kmer minhash mutations nanopore openmp
Last synced: 10 Nov 2024
https://github.com/edawson/mkmh
Generate kmers/minimizers/hashes/MinHash signatures, including with multiple kmer sizes.
kmer locality-sensitive-hashing minhash
Last synced: 10 Nov 2024
https://github.com/edawson/svaha2
Linear-time, low-memory construction of variation graphs
genome-graph genomics gfa structural-variation variation-graph
Last synced: 10 Nov 2024
https://github.com/edawson/svaha
Convert structural variants to sequence graphs [ VCF + FASTA ---> GFA ]
Last synced: 10 Nov 2024
https://github.com/edawson/check-sex
Determine the biological sex of a human whole-genome BAM file
Last synced: 10 Nov 2024
https://github.com/edawson/launchair
A small python utility which can execute a list of commands in parallel
Last synced: 10 Nov 2024
https://github.com/edawson/gram
Parse, manipulate, and emit GRAM (graph read alignment/map format)
Last synced: 10 Nov 2024
https://github.com/edawson/tidysig
A tidyverse-style package for plotting mutational signatures and context counts.
cancer-genomics ggplot2 mutational-signatures tidy-data tidyverse
Last synced: 10 Nov 2024
https://github.com/edawson/pliib
A hacky little C++ library that holds some useful functions.
Last synced: 10 Nov 2024
https://github.com/edawson/kseq_reader
A threadsafe + buffered fastq/fasta reading wrapper, based on kseq.h from Heng Li
Last synced: 10 Nov 2024
https://github.com/edawson/tinygfa
A header-only GFA file indexer (think .fai for GFA files)
Last synced: 10 Nov 2024
https://github.com/edawson/sv-exercise-1
A short exercise for learning to work with structural variants in VCF format
Last synced: 10 Nov 2024
https://github.com/edawson/biowulf-scripts
Scripts I use for analysis on NIH's Biowulf system.
Last synced: 10 Nov 2024
https://github.com/edawson/ggsv
Simulation scripts and other items for comparing SV callers
Last synced: 10 Nov 2024
https://github.com/edawson/seqmini
C++ code for creating minimizer indices on arbitrary FASTA / GFA
Last synced: 10 Nov 2024
https://github.com/edawson/libvcfh
A small library for generating VCF headers
Last synced: 10 Nov 2024
https://github.com/edawson/tinyfa
A header-only C++ FASTA parser and indexer
Last synced: 10 Nov 2024
https://github.com/edawson/sv-tutorial-2
A tutorial on calling structural variants with SVABA
Last synced: 10 Nov 2024
https://github.com/edawson/iplant-bwa-mem-parallel
A wrapper for increasing scaling of BWA.
Last synced: 10 Nov 2024
https://github.com/edawson/hpv_minion_analysis
Contains scripts used to analyze HPV samples sequenced on ONT minIONs.
Last synced: 10 Nov 2024
https://github.com/edawson/hpv_pangenome
Files and scripts for generating a pan-genome reference graph for learning models.
Last synced: 10 Nov 2024
https://github.com/edawson/cosmic2vcf
Convert various TSV files from the Catalogue of Somatic Mutations in Cancer to VCF (esp. structural variants)
Last synced: 10 Nov 2024
https://github.com/edawson/bed2vcf
Convert a BED file (and a FASTA reference) to *mostly* valid VCF.
Last synced: 10 Nov 2024
https://github.com/edawson/vg_learn
Datasets and scripts and general things for building machine learning tools with VG.
Last synced: 10 Nov 2024
https://github.com/edawson/cromrunner
A scheduler / meta-manager for running multiple Cromwell instances on a single WDL workflow in parallel.
Last synced: 10 Nov 2024
https://github.com/edawson/split-splice-fastq
A bit of python for slicing and splicing FASTA/FASTQ files.
Last synced: 10 Nov 2024
https://github.com/edawson/simple_mutator
A script for introducing mutations in a reference genome at specific rates.
Last synced: 10 Nov 2024
https://github.com/edawson/helpy
A random collection of python scripts which are easier than fighting the equivalent shell commands
Last synced: 10 Nov 2024
https://github.com/edawson/mkat-sclust
A compilable version of meerkat's sclust
Last synced: 10 Nov 2024
https://github.com/edawson/rkmh_sim_data
Example simulated data for rkmh (viral coinfection analysis using a MinHash toolkit)
Last synced: 10 Nov 2024
https://github.com/edawson/rov-spec
A pROVenance file format for data lineage (and universal computability)
Last synced: 10 Nov 2024
https://github.com/edawson/mkat-dre
A version of meerkat's dre that compiles.
Last synced: 10 Nov 2024
https://github.com/edawson/mirna_distributions
Scripts and code pertaining to "Human microRNAs Exhibit Two Distributions Within and Across Cancer Samples"
Last synced: 10 Nov 2024
https://github.com/edawson/mpakt
A small template-based library for binary I/O of C++ primitives and arrays.
Last synced: 10 Nov 2024
https://github.com/edawson/mkat-mybamtools
A modified version of the mybamtools library that actually compiles.
Last synced: 10 Nov 2024
https://github.com/edawson/ref_vcf_builder
A little bit of BASH to create a single standard reference VCF from several smaller ones.
Last synced: 10 Nov 2024
https://github.com/edawson/pyrov
CLI tools for writing ROV data provenance files
Last synced: 10 Nov 2024
https://github.com/edawson/novobreak-bin
A dummy repo for holding novobreak binaries
Last synced: 10 Nov 2024
https://github.com/edawson/mkat-bamreader
Fork of bamreader (from Meerkat) which actually compiles.
Last synced: 10 Nov 2024
https://github.com/edawson/mkat-bwa-0.6.2
A (patched, ancient) BWA version for meerkat
Last synced: 10 Nov 2024
https://github.com/edawson/iplant-gatk-qc
The scripts and JSON description necessary to produce a working iPlant version of GATK Realignment/Recalibration.
Last synced: 10 Nov 2024
https://github.com/edawson/maf_to_bed
Convert a maf file to a bed file to use with BEDtools.
Last synced: 10 Nov 2024
https://github.com/edawson/iplant-samtools-mpileup
The scripts and JSON descriptions necessary to run samtools mpileup on Stampede using iPlant
Last synced: 10 Nov 2024
https://github.com/edawson/fe
A python script/minimal GUI app for aggregating variant annotations and predicting impacts
Last synced: 10 Nov 2024
https://github.com/edawson/iplant-platypus
Contains the necessary files to create a working version of Platypus on iPlant
Last synced: 10 Nov 2024
https://github.com/edawson/bio_docker
Dockerfiles for several SV callers and other miscellaneous bio apps.
Last synced: 10 Nov 2024
https://github.com/edawson/storage-consumption-calculator
An R shiny app for calculating the energy used when storing a specified amount of data.
Last synced: 10 Nov 2024
https://github.com/edawson/biosandbox
Tools, scripts and programs for playing with biological data
Last synced: 10 Nov 2024
https://github.com/edawson/bamcov
BASH logic for generating a coverage-reduced BAM file
Last synced: 10 Nov 2024
https://github.com/edawson/iplant-bwa-index
Contains all of the bits and pieces needed to integrate BWA indexing into the iPlant environment.
Last synced: 10 Nov 2024
https://github.com/edawson/presig
Convert MAF files to formats used as input to mutational signature programs including SigProfiler
Last synced: 10 Nov 2024
https://github.com/edawson/sigprofilerhelper
Helper scripts for the SigProfiler suite of mutational signature analysis tools
Last synced: 10 Nov 2024
https://github.com/edawson/genelist_to_bed
Convert a list of genes to a bedfile
Last synced: 10 Nov 2024
https://github.com/edawson/firehose
A collection of scripts for munging genomic and epigenetic data from the Broad Firehose.
Last synced: 10 Nov 2024
https://github.com/edawson/cluster-svs
A wrapper around the PCAWG sv clustering scripts for per-project files.
Last synced: 10 Nov 2024
https://github.com/edawson/dawdl
WDL library for common bioinformatics tasks
Last synced: 10 Nov 2024
https://github.com/edawson/assisi
A somatic mutation signature simulator
autoencoders mutational-signatures simulation snvs
Last synced: 10 Nov 2024
https://github.com/edawson/vg_d
A docker file for vg (github.com/vgteam/vg), linked to an automatic build on Dockerhub.
Last synced: 10 Nov 2024
https://github.com/edawson/vcf_to_tidy_tsv
Convert VCF files to a tidy, tab-separated format
Last synced: 10 Nov 2024
https://github.com/edawson/firecloud-tools
Dockerfiles and WDL descriptions for various tools on Broad FireCloud
Last synced: 10 Nov 2024
https://github.com/edawson/tinyvcf
(The beginnings of) A small VCF parser with an emphasis on speed and simplicity.
Last synced: 10 Nov 2024
https://github.com/edawson/rkmh_paper_response
Code for running simulations for the RKMH paper review response
Last synced: 10 Nov 2024
https://github.com/edawson/submission_scripts
A bunch of helper scripts to make sense of the ludicrous LSF submission line.
Last synced: 10 Nov 2024
https://github.com/edawson/bammer
QC methods for checking if two BAM files from the same sample
Last synced: 10 Nov 2024
https://github.com/edawson/vg_pill
Contains source code for vg dependencies that are often installed via a package manager.
Last synced: 10 Nov 2024