GeMoSeq

GeMoSeq reconstructs genes and transcript models from mapped RNA-seq reads (in coordinate-sorted BAM format) and reports these in GFF format.

It is intended as a companion for the homology-based gene prediction program GeMoMa.

In a typical workflow, predictions of transcript models may be obtained from GeMoSeq for a collection of BAM files individually and subsequently merged using the GeMoMa Annotation Filter (GAF). Optionally, homology-based gene prediction may be performed using GeMoMa and the resulting GFF files may be merged using the Merge tool of GeMoSeq.

Command line tool

GeMoSeq is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose.

GeMoSeq and auxiliary tools are packaged in one runnable JAR that may be run from the command line with

java -jar GeMoSeq-1.2.3.jar

which lists the tools available and usage information

Available tools:

	gemoseq - GeMoSeq
	predictCDS - Predict CDS from GFF
	GAF - GeMoMa Annotation Filter
	Analyzer - Analyzer
	merge - Merge

Syntax: java -jar GeMoSeq-1.2.3.jar <toolname> [<parameter=value> ...]

Further info about the tools is given with
	java -jar GeMoSeq-1.2.3.jar <toolname> info

For tests of individual tools:
	java -jar GeMoSeq-1.2.3.jar <toolname> test [<verbose>]

Tool parameters are listed with
	java -jar GeMoSeq-1.2.3.jar <toolname>

You get a list of the tool parameters by calling GeMoSeq-1.2.3.jar with the corresponding tool name, e.g.,

java -jar GeMoSeq-1.2.3.jar gemoseq

The meaning of the individual tool parameters is described below. For convenience, we also include the GeMoMa tools Analyzer and GAF.

Source code

The source code of GeMoSeq is available from the Jstacs GitHub repository.

Examples

We give examples for applying GeMoSeq to a single sequencing library and for a larger-scale, integrated genome annotation together with GeMoMa GeMoSeq-Examples on a separate wiki page.

GeMoSeq

Prediction of transcript models using GeMoSeq.

GeMoSeq may be called with

java -jar GeMoSeq-1.2.3.jar gemoseq

and has the following parameters

name	comment	type
g	Genome (Genome sequence as FastA, type = fa,fna,fasta)	FILE
m	Mapped reads (Mapped Reads in BAM format, coordinate sorted, type = bam)	FILE
s	Stranded (Library strandedness, range={FR_UNSTRANDED, FR_FIRST_STRAND, FR_SECOND_STRAND}, default = FR_UNSTRANDED)	STRING
l	Longest intron length (Length of the longest intron reported, default = 100000)	INT
sil	Shortest intron length (Length of the shortest intron considered, default = 10)	INT
lr	Long reads (Long-read mode, default = false)	BOOLEAN
mnor	Minimum number of reads (Minimum number of reads required for an edge in the read graph, default = 1.0)	DOUBLE
mfor	Minimum fraction of reads (Minimum fraction of reads relative to adjacent exons that must support an intron in the enumeration, default = 0.01)	DOUBLE
mnoir	Minimum number of intron reads (Minimum number of reads required for an intron, default = 1.0)	DOUBLE
mfoir	Minimum fraction of intron reads (Minimum fraction of reads relative to adjacent exons for an intron to be considered, default = 0.01)	DOUBLE
p	Percent explained (Percent of abundance that must be explained by transcript models after quantification, default = 0.9)	DOUBLE
mrpg	Minimum reads per gene (Minimum abundance required for a gene to be reported, default = 40.0)	DOUBLE
mrpt	Minimum reads per transcript (Minimum abundance required for a transcript to be reported, default = 20.0)	DOUBLE
pa	Percent abundance (Minimum relative abundance required for a transcript to be reported, default = 0.05)	DOUBLE
sf	Successive fraction (Factor of the drop in abundance between successive transcript models, default = 20.0)	DOUBLE
mrl	Maximum region length (Maximum length of a region considered before it is split, default = 750000)	INT
mrc	Maximum region coverage (Maximum coverage in a region before reads are down-sampled, valid range = [0.0, Infinity], default = 100.0)	DOUBLE
mfgl	Maximum filled gap length (Maximum length of a gap filled by dummy reads, default = 50)	INT
q	Quality filter (Minimum mapping quality required for a read to be considered, default = 40)	INT
mpl	Minimum protein length (Minimum length of protein in AA, default = 70)	INT
gp	Gene prefix (Prefix to add to all gene names, default = G)	STRING
gnwc	Gene names with chromosome (If true, gene names will be constructed as <Gene prefix><chr>.<geneNumber>. Gene numbers will be assigned successively across all chromosomes., default = false)	BOOLEAN
outdir	The output directory, defaults to the current working directory (.)	STRING
threads	The number of threads used for the tool, defaults to 1. Currently, I/O of GeMoSeq runs on a single thread and runtime is limited by I/O performance. Hence, running GeMoSeq with a large number of threads is not recommended. On our infrastructure, a number of 6 threads has been the sweet spot.	INT

Example:

java -jar GeMoSeq-1.2.3.jar gemoseq g=<Genome> m=<Mapped_reads>

Predict CDS from GFF

Predict CDS from GFF may be called with

java -jar GeMoSeq-1.2.3.jar predictCDS

and has the following parameters

name	comment	type
g	Genome (Genome sequence as FastA, type = fa,fna.fasta)	FILE
p	predicted annotation ("GFF or GTF file containing the predicted annotation", type = gff,gff3,gff.gz,gff3.gz,gtf,gtf.gz)	FILE
m	Minimum protein length (Minimum length of protein in AA, default = 70)	INT
outdir	The output directory, defaults to the current working directory (.)	STRING

Example:

java -jar GeMoSeq-1.2.3.jar predictCDS g=<Genome> p=<predicted_annotation>

Merge

Merge may be called with

java -jar GeMoSeq-1.2.3.jar merge

and has the following parameters

name	comment	type
g	GeMoMa (GeMoMa predictions, type = gff,gff3)	FILE
GeMoSeq	GeMoSeq (GeMoSeq predictions, type = gff,gff3)	FILE
m	Mode (, range={intersect, union, intermediate, annotate}, default = intersect)	STRING
	No parameters for selection "intersect" No parameters for selection "union" Parameters for selection "intermediate": GeMoMa-strict GeMoMa-strict (GeMoMa predictions with strict settings, type = gff,gff3) FILE GeMoSeq-strict GeMoSeq-strict (GeMoSeq predictions with strict settings, type = gff,gff3) FILE Parameters for selection "annotate": GeMoMa-strict GeMoMa-strict (GeMoMa predictions with strict settings, type = gff,gff3) FILE GeMoSeq-strict GeMoSeq-strict (GeMoSeq predictions with strict settings, type = gff,gff3) FILE l Low-confidence (include low-confidence predictions, default = true) BOOLEAN
outdir	The output directory, defaults to the current working directory (.)	STRING

Example:

java -jar GeMoSeq-1.2.3.jar merge g=<GeMoMa> GeMoSeq=<GeMoSeq>

Version history

• Version 1.2.3 (2025/11/11): Renamed the tool to GeMoSeq and improved prediction from long-read data
• Version 1.2.1 (2025/05/28): improved handling of exceptions in multi-thread mode
• Version 1.2 (2025/05/12): changes in the following tools
  • gemorna: fixed a problem where (incomplete) CDS would be predicted in transcripts without any proper stop codon
• Version 1.1 (2025/04/15): changes in the following tools
  • merge: include flag if low-confidence predictions will be included in "annotate" mode
  • gemorna: allow to provide custom prefix for gene names and to include the chromosome into the gene names
• Version 1.0: initial version of GeMoRNA