DNA Sequencing

DNA Sequence Quality

DNA Sequence Quality - Phred - provides base calling, chromatogram display and high quality sequence region evaluation and presentation for up to five sequences simultaneously.

Sequence assembly - you don't need your own contig assembly program when you can use:

Galaxy for Genome Assembly

Galaxy for Genome Assembly - The Genome Assembly Workbench is a comprehensive set of analysis tools and consolidated workflows to assist in Genome Assembly. The workbench is based on the Galaxy framework, which guarantees simple access, easy extension, flexible adaption to personal and security needs, and sophisticated analyses independent of command-line knowledge. requires free registration.

CAP3

CAP3 (PBIL, France ),
(Reference: Huang,X. & Madan A. 1999. Genome Res.9: 868-877).

MicroScope web site

MicroScope web site (hosted at Genoscope), provides an environment for expert annotation and comparative genomics. Genome project: Annotation and comparative analyses of finished or draft genome sequences. For pre-annotated sequences, they only integrate annotations from NCBI RefSeq complete genome section. Metagenome project: Annotation and comparative analyses of assembled metagenomic sequences. Currently, they are able to integrate datasets below 20 Mb of contigs per bin.

EGassember

EGassember - aligns and merges sequence fragments resulting from shotgun sequencing or gene transcripts (EST) fragments in order to reconstruct the original segment or gene
(Reference: A. Masoudi-Nejad et al. 2006. Nucl. Acids Res. 34: W459-462).

NanoPipe

NanoPipe - was developed in consideration of the specifics of the MinION sequencing technologies, providing accordingly adjusted alignment parameters. The range of the target species/sequences for the alignment is not limited, and the descriptive usage page of NanoPipe helps a user to succeed with NanoPipe analysis. The results contain alignment statistics, consensus sequence, polymorphisms data, and visualization of the alignment.
(Reference: Shabardina V et al. (2019) Gigascience 8(2). pii: giy169).

COV2HTML

COV2HTML: a visualization and analysis tool of bacterial next generation sequencing (NGS) data for postgenomics life scientists - allows performing both coverage visualization and analysis of NGS alignments performed on prokaryotic organisms (bacteria and phages). It combines two processes: a tool that converts the huge NGS mapping or coverage files into light specific coverage files containing information on genetic elements; and a visualization interface allowing a real-time analysis of data with optional integration of statistical results.
(Reference: Monot M. et al. 2014. OMICS 18(3): 184-95).

PhageTerm

PhageTerm - is a fast and user-friendly software package which can be used to determine bacteriophage termini and packaging mode from randomly fragmented NGS data. It is part of the Galaxy package, and can be found in the "NGS: Mapping" directory. Ideal is you want an automated answer.
(Reference: Garneau JR, et al. 2017. Sci Rep. 7(1):8292).

Sequencing errors:

if your DNA sequence doesn't match the expected protein sequence you can check for errors using BLASTx which compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors. Other programs include:

FrameD

FrameD - is a program that predicts coding regions in prokaryotic and matured eukaryotic sequences. Initially targeted at gene prediction in bacterial GC rich genomes, the gene model used in FrameD also allows to predict genes in the presence of frameshifts and partially undetermined sequences which makes it also very suitable for gene prediction and frameshift correction in unfinished sequences such as EST and EST cluster sequences. Like recent eukaryotic gene prediction programs, FrameD also includes the ability to take into account protein similarity information both in its prediction and its graphical output.
(Reference: T. Schliex et al. 2003. Nucl. Acids Res. 31: 3738-3741)

PATH

PATH: protein back-translation and alignment - addresses the problem of finding distant protein homologies where the divergence is the result of frameshift mutations and substitutions. Given two input protein sequences, the method implicitly aligns all the possible pairs of DNA sequences that encode them, by manipulating memory-efficient graph representations of the complete set of putative DNA sequences for each protein.
(Reference: Gîrdea M et al. 2010. Algorithms for Molecular Biology 5:)

In-silico.com

In-silico.com (Dr. Joseba Bikandi & co-workers, Faculty of Pharmacy, in the University of the Basque Country) - allows in silico experiments including theoretical PCR amplification, AFLP-PCR , restriction analysis and pulsed field gel electrophoresis [PFGE] with bacterial & archael genomes found in the public database.

Updated: December, 2025