ksahlin

ksahlin's Stars

• Cyan4973/xxHash

  Extremely fast non-cryptographic hash algorithm

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• snakemake/snakemake

  This is the development home of the workflow management system Snakemake. For general information, see

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• skarupke/flat_hash_map

  A very fast hashtable

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• marbl/CHM13

  The complete sequence of a human genome

  909689498

• chaimleib/intervaltree

  A mutable, self-balancing interval tree. Queries may be by point, by range overlap, or by range containment.

  Language:Python6311798106

• mortberg/cubicaltt

  Experimental implementation of Cubical Type Theory

  Language:Haskell568456176

• lh3/minigraph

  Sequence-to-graph mapper and graph generator

  Language:C4102910939

• PacificBiosciences/pbbioconda

  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.

  2492970044

• lh3/kmer-cnt

  Code examples of fast and simple k-mer counters for tutorial purposes

  Language:C++16310915

• rvaser/spoa

  SIMD partial order alignment tool/library

  Language:C++158165132

• smarco/WFA2-lib

  WFA-lib: Wavefront alignment algorithm library v2

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• dzhang32/ggtranscript

  Visualizing transcript structure and annotation using ggplot2

  Language:R1303139

• arvestad/alv

  A console-based alignment viewer

  Language:Python10731613

• jermp/sshash

  A compressed, associative, exact, and weighted dictionary for k-mers.

  Language:C++8352117

• nanoporetech/pychopper

  A tool to identify, orient, trim and rescue full length cDNA reads

  Language:Python79235722

• shenwei356/unikmer

  A versatile toolkit for k-mers with taxonomic information

  Language:Go753227

• ekimb/mapquik

  Efficient low-divergence mapping of long reads in minimizer space

  Language:Rust625124

• cartoonist/kseqpp

  Fast FASTA/Q parser and writer (C++ re-implementation of kseq library)

  Language:C++452108

• richarddurbin/modimizer

  a toolset for fast DNA read set matching and assembly using a new type of reduced kmer

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• lexnederbragt/developments-in-next-generation-sequencing

  Developments in next generation sequencing: instruments, read lengths, throughput. See

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• bioinf-benchmarking/mapping-benchmarking

  Snakemake pipeline for benchmarking read mappers

  Language:Python16431

• aljpetri/isONform

  De novo construction of isoforms from long-read data

  Language:Python15292

• kamimrcht/CARNAC-LR

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• nanoporetech/isONclust2

  A tool for de novo clustering of long transcriptomic reads

  Language:C++141673

• shenwei356/strobemers

  A Go implementation of the strobemers (https://github.com/ksahlin/strobemers)

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• fjdf/slaMEM

  Finding Maximal Exact Matches (MEMs) using a Sampled LCP Array

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• BGI-Qingdao/strobemer_cpptest

  An c++ implemention of strobemer

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• Moein-Karami/RandStrobes

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• RongxingWong/AcceleratingSplicedAlignment

  Accelerating spliced alignment of long RNA sequencing reads using parallel maximal exact match retrieval

  10

• ThomasBaudeau/periscope_multifasta

  A tool to quantify sub-genomic RNA (sgRNA) expression in SARS-CoV-2 artic network amplicon nanopore sequencing data.

  Language:Python110