ORFik

gffcompare -- Tool for comparing, merging, and annotating RNA-seq transcript assemblies against a reference annotation. Classifies each assembled transcript with a class code (=, c, j, u, x, i, p, r,

1 shared topic • 2 shared operations

MAKER — portable genome annotation pipeline that integrates ab initio gene predictors (SNAP, Augustus, GeneMark), protein and EST evidence alignment, and repeat masking to produce GFF3 gene models wit

1 shared topic • 2 shared operations

MGI/GXD (Mouse Genome Informatics / Gene Expression Database) — authoritative resource for mouse genetics, genomics, and gene expression data maintained by The Jackson Laboratory. Provides comprehensi

1 shared topic • 2 shared operations

Qualimap — platform-independent quality control tool for next-generation sequencing alignment data. Provides BAM QC (coverage, insert size, GC content, mapping quality), RNA-seq QC (gene body coverage

1 shared topic • 2 shared operations

RASQUAL (Robust Allele Specific QUantification and quality controL) — joint QTL mapping tool that integrates total read counts and allele-specific reads for cis-regulatory variant discovery. Detects i

1 shared topic • 2 shared operations