This is your work, valued

Rennes, France

Karel Břinda

Expert
@karel-brinda

Bioinformatics, Algorithms, Genomics, Pathogens, Rapid Diagnostics, and Antibiotic Resistance

MiniPhy. Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]

48

ococo. Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.

46

Phylign. Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)

41

smbl. SMBL - SnakeMake Bioinformatics Library. Automatic installation of bioinformatics software in your SnakeMake pipelines.

23

samsift. SAMsift: advanced filtering and tagging of SAM/BAM alignments using Python expressions.

23

NanoSim-H. NanoSim-H: a simulator of Oxford Nanopore reads; a fork of NanoSim.

18

rnftools. RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.

14

attotree. Rapid estimation of phylogenetic trees using sketching

13

svg42pdf. Python

6

tp-zpevnik. Zpěvník Technické přestávky. Výsledné (automaticky generované) zpěvníky se nachází na http://karel-brinda.github.io/tp-zpevnik/.

5

ligm-business-cards. LaTeX and OpenOffice templates for business cards.

5

phylogenetic-compression-supplement. Supplementary repository for "Efficient and robust search of microbial genomes via Phylogenetic Compression"

4

fasta2kmers. A simple program to split sequences from a FASTA/FASTQ file into k-mers in the FASTA format.

3

dymas. Dynamic Mapping Simulator.

3

random-genome. A simple program to generate a high-entropy random genome

3

harvard-clusters-example. A simple Snakemake pipeline that can be run on all three Harvard clusters

2

galitime. Software for benchmarking scientific software.

2

cmake-ext. CMake external projects.

2

unprotect-docx. Bash script to unprotect password-protected unencrypted DOCX documents.

1

oneliners. Useful bash one-liners for bioinformatics.

1

masked-superstrings-supplement. Python

1

dbgfm. C

1

Awesome-Bioinformatics. A curated list of awesome Bioinformatics libraries and software.

1

simplitigs-supplementary. Data and pipelines for Simplitigs as an efficient and scalable representation of de Bruijn graphs

1

metameda. MetaMedA: meta-analysis using PubMed

1