Karel Břinda (@karel-brinda)
github

karel-brinda

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  • Stars
    star
    208
  • Global Rank 118,910 (Top 5 %)
  • Followers 169
  • Following 285
  • Registered about 10 years ago
  • Most used languages
    Python
         52.4 %
    TeX
         9.5 %
    C++
         9.5 %
    C
         4.8 %
    Makefile     4.8 %
    HTML
         4.8 %
    Shell
         4.8 %
    CMake     4.8 %
    R
         4.8 %
  • Location 🇺🇸 United States
  • Country Total Rank 30,191
  • Country Ranking
    CMake     693
    TeX
         1,129
    Makefile     2,532
    C++
         3,946
    Python
         7,177
    R
         9,359

Top repositories

1

ococo

Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.
C++
47
star
2

Phylign

Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)
Python
25
star
3

samsift

SAMsift: advanced filtering and tagging of SAM/BAM alignments using Python expressions.
Python
23
star
4

smbl

SMBL - SnakeMake Bioinformatics Library. Automatic installation of bioinformatics software in your SnakeMake pipelines.
Python
23
star
5

NanoSim-H

NanoSim-H: a simulator of Oxford Nanopore reads; a fork of NanoSim.
Python
16
star
6

MiniPhy

Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]
Python
14
star
7

rnftools

RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.
Python
14
star
8

svg42pdf

Python
6
star
9

ligm-business-cards

LaTeX and OpenOffice templates for business cards.
TeX
6
star
10

attotree

Rapid estimation of phylogenetic trees using sketching
Python
6
star
11

tp-zpevnik

Zpěvník Technické přestávky. Výsledné (automaticky generované) zpěvníky se nachází na http://karel-brinda.github.io/tp-zpevnik/.
TeX
5
star
12

dymas

Dynamic Mapping Simulator.
HTML
3
star
13

random-genome

A simple program to generate a high-entropy random genome
C++
3
star
14

fasta2kmers

A simple program to split sequences from a FASTA/FASTQ file into k-mers in the FASTA format.
C
3
star
15

de-MiniPhy-BIGSIdata

Client for downloading and a phylogenetic decompression of the BIGSIdata de Bruijn graphs
Python
3
star
16

cmake-ext

CMake external projects.
CMake
2
star
17

harvard-clusters-example

A simple Snakemake pipeline that can be run on all three Harvard clusters
Makefile
2
star
18

galitime

Software for benchmarking scientific software.
Python
2
star
19

simplitigs-supplementary

Data and pipelines for Simplitigs as an efficient and scalable representation of de Bruijn graphs
R
1
star
20

metameda

MetaMedA: meta-analysis using PubMed
Python
1
star
21

unprotect-docx

Bash script to unprotect password-protected unencrypted DOCX documents.
Shell
1
star