alshai
Senior Bioinformatics Scientist @ Illumina Formerly PhD Student @ JHU CS, Langmead Lab.
Illumina San Diego
Pinned Repositories
Big-BWT
modified from gitlab.com/manzai/Big-BWT to support fasta files
bioconda-recipes
Conda recipes for the bioconda channel.
bioconda-utils
Utilities for building and managing bioconda recipes
hts_utils
C++ library and recipes for handling high-throughput sequencing data. Requires htslib
levioSAM
Lift-over alignments from variant-aware references
pfbwt-f
Prefix Free Parsing Algorthim for building BWTs for genomic data
r-index
An optimal space run-length Burrows-Wheeler transform full-text index
rowbowt
run-length BWT tools for genomic sequences
varcount
Outputs alignment coverage over a predefined set of variants
vcf2msa
convert a multi-sample VCF file to a multiple sequence alignment (C)
alshai's Repositories
alshai/levioSAM
Lift-over alignments from variant-aware references
alshai/r-index
An optimal space run-length Burrows-Wheeler transform full-text index
alshai/rowbowt
run-length BWT tools for genomic sequences
alshai/vcf2msa
convert a multi-sample VCF file to a multiple sequence alignment (C)
alshai/Big-BWT
modified from gitlab.com/manzai/Big-BWT to support fasta files
alshai/pfbwt-f
Prefix Free Parsing Algorthim for building BWTs for genomic data
alshai/varcount
Outputs alignment coverage over a predefined set of variants
alshai/hts_utils
C++ library and recipes for handling high-throughput sequencing data. Requires htslib
alshai/bioconda-recipes
Conda recipes for the bioconda channel.
alshai/bioconda-utils
Utilities for building and managing bioconda recipes
alshai/bowtie
An ultrafast memory-efficient short read aligner
alshai/bwtstats
prints out some relevant stats related to the Burrows-Wheeler Transform (BWT) of a sequence
alshai/genome_inference
snakemake workflow for creating a personal genome through low-coverage imputation.
alshai/gramtools
Genome inference from a population reference graph
alshai/ips4o
In-place Parallel Super Scalar Samplesort (IPS⁴o)
alshai/nanopolish
Signal-level algorithms for MinION data
alshai/pysdsl
Python bindings to Succinct Data Structure Library 2.0
alshai/ssw-rs
Striped Smith Waterman implementation using Rust and SIMD instructions
alshai/westwing_sentiment
A sentiment analysis model for The West Wing
alshai/wfa-rs
Rust implementation of Wavefront pairwise alignment algorithm (WFA)