Geo Pertea (@gpertea)
github

gpertea

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  • Stars
    star
    829
  • Global Rank 36,652 (Top 2 %)
  • Followers 134
  • Following 7
  • Registered almost 12 years ago
  • Most used languages
    C++
         82.4 %
    R
         5.9 %
    C
         5.9 %
    Perl
         5.9 %
  • Location ๐Ÿ‡บ๐Ÿ‡ธ United States
  • Country Total Rank 10,118
  • Country Ranking
    C++
         500
    Perl
         1,692
    R
         7,856

Top repositories

1

stringtie

Transcript assembly and quantification for RNA-Seq
C++
358
star
2

gffread

GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
C++
305
star
3

gffcompare

classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
C++
151
star
4

gclib

GCLib - Genomic C++ library of reusable code for bioinformatics projects
C++
29
star
5

mgblast

fast all-vs-all DNA alignment tool, modification of megablast from a 2006 version of NCBI C Toolkit
C
7
star
6

cdbfasta

Constant DataBase tools for indexing and retrieving records from multi-FASTA or similarly structured files
C++
7
star
7

gsrc

various sources and scripts for genomic research software
C++
6
star
8

gscripts

mish-mash of scripts I have been using in genomics (bioinformatics) or IT/engineering
Perl
5
star
9

fqtrim

filtering and trimming next generation sequencing reads
C++
4
star
10

tiebrush

summarize and filter read alignments from multiple sequencing samples (taken as sorted BAM files)
C++
4
star
11

bamread

basic SAM/BAM/CRAM file reading/writing (and C++ wrapper classes) using HTSlib API
C++
4
star
12

pwasm

MSA and consensus (assembly) generator from pairwise alignments of DNA sequences
C++
2
star
13

CNView

CNView wrapper
R
1
star
14

CuffCompare

compare results and evaluate the accuracy of RNA-Seq transcript assemblers (Cufflinks, Stringtie)
C++
1
star
15

trmap

mass transcript classification by streaming GFF/BED over reference GFF/BED
C++
1
star
16

mblasm

consensus (assembly) generator from mgblast (modified megablast) pairwise alignments
C++
1
star
17

gsegindex

Testing genomic segment index for fast intersection queries
C++
1
star