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intervaltree
a minimal C++ interval tree implementation
alignment-and-variant-calling-tutorial
basic walk-throughs for alignment and variant calling from NGS sequencing datafraction.js
A fraction math library in javascript.seqwish
alignment to variation graph inducerfastahack
utilities for indexing and sequence extraction from FASTA filesbamaddrg
adds sample names and read-group (RG) tags to BAM alignmentsglia
a string to graph alignerthesis
my PhD thesisedyeet
base-accurate DNA sequence alignments using edlib and mashmap2split
split and join for C++ stringsgimbricate
recompute GFA link overlapsmmmulti
memory mapped multimap, multiset, and implicit interval tree based on an in-place parallel sortmultichoose
generate multiset combinations (n multichoose k)impg
implicit pangenome graphpafplot
base-level dotplots from PAF alignmentsHLA-zoo
genome variation graphs constructed from HLA GRCh38 ALTsguix-genomics
guix packages for bioinformatics softwaremultipermute
efficient multiset permutations1000G-integration
variant integration methods for the 1000 Genomes Projecthhga
haplotypes genotypes and alleles example decision synthesizergafpack
convert variation graph alignments to coverage maps over nodesogap
gap opening realigner for BAM data streamsviral-assembly
exploring viral genome assembly with variation graph toolsshuntingyard
implementations of Dijkstra's shunting-yard algorithm for infix notation parsingsmithwaterman
smith-waterman-gotoh alignment algorithmdrawbwt
vector illustrations of BWT based searching on small stringsmutatrix
genome simulation across a population with zeta-distributed allele frequency, snps, insertions, deletions, and multi-nucleotide polymorphismspca
PCA in rustssh.py
synchronous, serial, and parallel ssh, scp, and ping methods in pythonbitcoin-fs
encode arbitrary data in bitcoin transactionswflign
the we-flyin WFA-guided ultralong tiling sequence alignerACAD18
Day 2 of ACAD's 2018 Advanced Bioinformatics Workshopsuccinct-graph
compressed, queryable variation graphsopenconnect-sso-docker
connect to a cisco anyconnect server with 2FA via web SSO on a headless serverfastix
Prefix-renaming FASTA records really fast.dozyg
sequence to graph mapperhapviz
indel haplotype visualization on the command line from BAM filesyllm
Yet another LLM command line interfaceUSDA-SR22-importer
assists in importing the USDA's SR22 nutritional database from MS Access to MySQLfoxsamply
algorenderer / a script to convert FoxDot code to recorded samplesyeast-pangenome
yeast pangenomesplitfa
split a FASTA sequence file into shorter sequenceswflambda
WFλ - wavefront alignment with callback match functionbkmers
binary kmers written numericallyhamming-fasta
brute force online sequence similarity searchgaffy
GAF (graph alignment format) command line utilityinterleave-fastq
interleaves fastq files (also gzipped ones!)beats
snippets of music in foxdotarfer
annotation of variants using genotype likelihoodskmers
generate kmer frequency information from text streamsxbzipLib
XBzip/XBWT implementation from "Compressing and indexing labeled trees, with applications," P Ferragina et al.jvcf
Joint Variant Call Format -- JSON notation for genetic variant annotationrsvd
rSVD in rustbamprofile
profiles alignment mismatches and gapsdirtyzipf
zipfian int distributions using a fast approximation for powatomicbitvector
atomic bitset/bitvector with size determined at runtime3q29
3q29 pangenome build from HPRC year 1 samplessgd2
header-only large graph layout via stochastic gradient descentpafcov
pairwise alignment file coverage metricpafnet
PAF alignment to network format converterparyfor
parallel_for based on atomic queues and C++11 threadsphred.py
phred quality conversion to and from float and log spaceintervalstab
interval stabbing (pointwise range lookup) using the FastStabbing algorithmedlign
exploring identity-based alignment chaininggraphappy
a variation graph-oriented fork of WhatsHaplru_cache
A thread-safe LRU cache implementation in C++aptertree
Apter Trees in rustpoa-motifs
exploring variation graph models for motifs based on partial order alignmentkmerj
kmer counting comparisons in low memoryentropy
shannon entropyssw
striped smith waterman implementationdatscriptish
it's kind've like make, but not really. and it's for streams!simgenie
diplotype caller simulation on pangenie and freebayesdrosophila
drosophila genome assembly and analysistsvtools
tools for manipulating tab-separated-values files, mostly in C++endian
c++ header library for manipulating endiannessuniqprimers
determines if the primers required to assay VCF records are unique (provided BAM alignments of the primers and a VCF file of the variants)shastaGFA
scripts for interpreting GFAs made by the shasta assemblerwikiq
an xml to .tsv converter for wikimedia XML data dumpsleveldb-snappy
demonstrates how to build leveldb with snappy support using the static libraries for each and git submodulesvatfilter
extensions for manipulating VCF files annotated with the Variant Annotation Tool (VAT)gprof-compare
compare call counts in two gprof profile outputsqllm
query local LLM openai-API-compatible endpointstsvsplit
split tsv files with headersgenmusic
subarch-select
pick an executable based on CPU capabilitiesbad-python-list
equal lists should serialize equally, but don'tphage
phage assembly and analysis scriptsgatk-swe
factorial-ln
compute log(n!) of huge numbersbamquality
read quality distributions for BAM and FASTQ filesstrswap
command line tool to swap string patterns in text filesdiatoms
contig ordering using linkage disequilibriumembeddna
test of DNA embeddings using a transformerprotobufstream
protocol buffers streamstidalcycles-stream
stream a multiuser tidalcycles sessionsautocorr
estimating autocorrelation in sequences with the goal of finding repeat subunits in DNAfasta-utilities
utility scripts and programs for manipulating fasta fileshexygraph
a hexastore in C++ using leveldbfasta-to-fastq
Automatically exported from code.google.com/p/fasta-to-fastqLove Open Source and this site? Check out how you can help us
