gpertea/gsegindex

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C++
Created over 3 years ago
Updated over 3 years ago

gpertea/gsegindex

gpertea

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Testing genomic segment index for fast intersection queries

stringtie

Transcript assembly and quantification for RNA-Seq

gffread

GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more

gffcompare

classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF

gclib

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

mgblast

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

cdbfasta

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

gsrc

various sources and scripts for genomic research software

gscripts

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

fqtrim

filtering and trimming next generation sequencing reads

tiebrush

summarize and filter read alignments from multiple sequencing samples (taken as sorted BAM files)

bamread

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

pwasm

MSA and consensus (assembly) generator from pairwise alignments of DNA sequences

CNView

CuffCompare

compare results and evaluate the accuracy of RNA-Seq transcript assemblers (Cufflinks, Stringtie)

trmap

mass transcript classification by streaming GFF/BED over reference GFF/BED

mblasm

consensus (assembly) generator from mgblast (modified megablast) pairwise alignments