gffcompare

Use when merging multiple Cufflinks transcript assemblies into a unified transcriptome for downstream differential expression analysis with Cuffdiff. Covers the full Cuffmerge workflow: creating assem

1 shared topic • 2 shared operations

gffread -- GFF/GTF utility for filtering, converting, and extracting sequences from genome annotation files. Converts between GFF3 and GTF formats, extracts transcript (FASTA) and protein sequences fr

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

Rcorrector — kmer-based error correction for RNA-seq reads. Corrects Illumina sequencing errors in FASTQ data using Jellyfish2 bloom filters and adaptive kmer frequency thresholds. Handles non-uniform

1 shared topic • 2 shared operations

Trinity — de novo transcriptome assembler for RNA-seq data. Reconstructs full-length transcript isoforms without a reference genome using three sequential modules: Inchworm (greedy k-mer assembly), Ch

1 shared topic • 2 shared operations