Table 1.

Selected tools for transcript assembly

Process	Tool	Purpose	Input	Output
Read treatment	FastQC	Checks the integrity and quality of reads	Fastq files	Quality charts
	FastX toolkit, Flexbar, Trimommatic	Filters or trims reads	Fastq files	Clean reads; reports
Assembly	Trinity, Trans-ABySS, Oases, SSP, IDBA-tran	Assembles reads without reference	Clean reads	Assembled transcripts
	TOPHAT, STAR, HISAT, HISAT2 with stringTie	Assembles reads with reference annotation	Clean reads, genomic reference, reference annotation	Assembled transcripts
Transcript Classification	BEDtools, glBase	Checks overlap between coordinates	BED, GTF, GFF files	BED, GTF, GFF, report files
	BLAST, BLAT, GMAT, Augustus	Homology based classification	Fatsa files	Alignments, reports
	CPAT, FEELnc, NRC, lncRScan-SVM	Coding potential assessment	GTF or fasta files; reference annotations (mRNA fasta or GTF and genomic fasta)	Coding potential scores, reports
Mapping	TOPHAT, STAR, HISAT, HISAT2, Bowtie, BWA	Aligns reads to transcript or genes	Reads; reference annotations (gtf)	Alignments (bam, sam)
Quantification	RSEM, StringTie, bam-readcount, featureCount	Estimates transcript abundance	Alignment files	Abundance estimates
	Sailfish, Salmon, Kallisto	Estimates abundance without alignment	Reads; reference annotations	Abundance estimates