gpertea/gscripts

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Rank 2,861,937 (Top 57 %)
Language
Perl
License
The Unlicense
Created about 8 years ago
Updated over 1 year ago

gpertea/gscripts

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

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

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

gsegindex

Testing genomic segment index for fast intersection queries