blachlylab

All

44 repositories

mucor3
Public
Parses VCF data into tabular spreadsheets and aggregates data by sample
bioinformatics vcf aggregation jsonlines
D
•
MIT License
•0•0•9•0•Updated Feb 7, 2023Feb 7, 2023
koalas
Public
Ad hoc Data Frames
D
•0•0•1•0•Updated Nov 16, 2022Nov 16, 2022
typesafe-coordinates
Public
Typesafe Coordinate Systems in High-Throughput Sequencing Applications
TeX
•0•1•6•0•Updated Sep 13, 2022Sep 13, 2022
dhtslib
Public
D bindings and OOP wrappers for htslib
bioinformatics d dlang next-generation-sequencing
D
•
MIT License
•1•7•23•1•Updated Sep 4, 2022Sep 4, 2022
blachlylab.github.io
Public
https://blachlylab.github.io/
HTML
•0•0•0•0•Updated Aug 1, 2022Aug 1, 2022
nbib-rs
Public
MEDLINE/Pubmed .nbib format to CSL-JSON conversion
Rust
•0•0•2•0•Updated Apr 9, 2022Apr 9, 2022
recontig
Public
Dynamic Contig Nomenclature Reassignment
D
•
MIT License
•1•1•7•0•Updated Mar 22, 2022Mar 22, 2022
fade
Public
Fragmentase Artifact Detection and Elimination
bioinformatics enzyme dlang next-generation-sequencing fragmentation
D
•
MIT License
•3•11•8•0•Updated Mar 22, 2022Mar 22, 2022
dlang-static-docker
Public
Build static D binaries with docker
bioinformatics dlang docker
Dockerfile
•
MIT License
•0•0•0•0•Updated Feb 6, 2022Feb 6, 2022
blachlylab-old-github-io
Public
HTML
•0•0•0•0•Updated Jan 15, 2022Jan 15, 2022
nopilesum
Public
Alternative to GATK4's GetPileupSummaries using allele counting
bioinformatics
D
•
MIT License
•0•0•1•0•Updated Jan 6, 2022Jan 6, 2022
dparasail
Public
Dlang Bindings for the Parasail alignment library.
dlang alignment
D
•
MIT License
•0•0•0•0•Updated Jan 3, 2022Jan 3, 2022
nbib
Public
MEDLINE/Pubmed .nbib format to CSL-JSON conversion
D
•
MIT License
•0•0•0•0•Updated Oct 11, 2021Oct 11, 2021
cadd2vcf
Public
A tool to modify VCFs with CADD score output
bioinformatics ngs vcf
D
•0•0•1•0•Updated Aug 25, 2021Aug 25, 2021
fishnet
Public
Filter multi-read fast5 files
bioinformatics nanopore-sequencing
D
•0•0•4•0•Updated Jul 1, 2021Jul 1, 2021
gff3d
Public
GFF3 parser in D / dlang
bioinformatics next-generation-sequencing
D
•
MIT License
•0•0•2•0•Updated May 8, 2021May 8, 2021
fastq-grow
Public
Lengthen the sequences in FASTQ files
bioinformatics fastq
D
•
GNU General Public License v3.0
•0•0•2•0•Updated May 4, 2021May 4, 2021
swiftover
Public
Fast liftover
bioinformatics genomics genome d dlang liftover
D
•
GNU General Public License v3.0
•0•1•11•1•Updated Feb 24, 2021Feb 24, 2021
intervaltree
Public
Interval tree structures in D
avl-tree genomics data-structures interval-tree binary-trees splay-trees
D
•
MIT License
•0•7•9•0•Updated Feb 23, 2021Feb 23, 2021
maskerade
Public
N mask BAM file according to BED regions
bam-files bioinformatics sequencing
D
•0•0•0•0•Updated Feb 2, 2021Feb 2, 2021
dklib
Public
D ports of klib algorithms
D
•
MIT License
•5•5•2•1•Updated Aug 30, 2020Aug 30, 2020
SABER
Public
SABER: Selection of Amplicon Barcodes from Experimental Replicates
bioinformatics zebrafish
R
•
MIT License
•1•0•0•0•Updated Feb 7, 2020Feb 7, 2020
stdq
Public
Route stdin/stdout through ZeroMQ
zeromq
C
•
MIT License
•1•0•3•0•Updated Nov 3, 2019Nov 3, 2019
cgranges
Public
A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)
C
•
MIT License
•18•0•0•0•Updated Aug 18, 2019Aug 18, 2019
vcf_atomizer
Public
Parses a VCF file into line-delimited json
golang json bioinformatics vcf jsonlines
Go
•
MIT License
•0•0•2•0•Updated Jun 26, 2019Jun 26, 2019
depthGauge
Public
bioinformatics variant-calling
D
•
MIT License
•0•0•0•0•Updated Jun 25, 2019Jun 25, 2019
GLO
Public
Go Language implementation of LiftOver
bioinformatics liftover
Go
•1•7•6•0•Updated May 9, 2019May 9, 2019
bedcov-it
Public
benchmark interval tree impl's with ersatz bedtools cov
benchmark bioinformatics
D
•
MIT License
•0•0•0•0•Updated May 3, 2019May 3, 2019
dksw2
Public
D bindings for ksw2
bioinformatics next-generation-sequencing alignment
D
•0•0•0•0•Updated Apr 5, 2019Apr 5, 2019
pyega
Public
EGA (European Genome-phenome archive) downloader
Python
•
Apache License 2.0
•3•0•0•0•Updated Jan 27, 2019Jan 27, 2019