asfenshopper.blogg.se - Serial cloner alternative

SERIAL CLONER ALTERNATIVE SOFTWARE
SERIAL CLONER ALTERNATIVE FREE

Lighter - Lighter: fast and memory-efficient sequencing error correction without counting.Fiona - Fiona: A parallel and automatic strategy for read error correction.Racer (Illumina only) - Supersedes HiTek by the same authors.Results in a substantial improvement in subsequent assembly steps. Quake - corrects sequencing reads or throws out bad reads.Pollux - claims to be able to do many platforms, including Illumina and Ion Torrent.FASTX-Toolkit - Pre-processing tools for sequencing reads.Web site with links to error correction tools. A bunch of nice tools for short read overlapping, trimming QC etc. BBMap - short read aligner, 100% Java.Some programs of this type also merge reads from both pairs of a fragment. Trimming, elimination of small fragments etc. There seems to be no reason to have Samstat when FastQC is available. The graphs are less useful than what FastQC presents.

Generally, gives some of the same information as FastQC, but doesn't present overall numerical statistics, nor k-mer information.

Samstat - (v 1.5.1) command line program to generate QC reports on reads.

Can save QC information in a nice HTML report.

DONE FastQC - GUI for evaluating raw or corrected read files.

Genome Assembly Pre-processing Quality control and assessment

Need to have a good 3D structure viewer.

One possibility would be ot modify PROT2NUC to make a list of the best primers, and then to overline them on the output.

Reverse translation - There should be an automated way to identify the best degnerate primers from a protein sequence.

However, it looks like the last release was in 2011. Includes blastviewer for viewing blast results.

SERIAL CLONER ALTERNATIVE SOFTWARE

EPoS - a modular software framework for phylogenetic analysis and visualization.

SERIAL CLONER ALTERNATIVE FREE

CLC Sequence Viewer - free Linux, Windows, Mac.They include things like Jdotplotter, SequenceSearcher, NAP (DNA to protein aligner?), GraphDNA. The Viral Bioinformatics Resource Center at UVic has a bunch of neat Java applications that look quite promising.GenomeTools - looks particularly good for tools.Ugene - Especially good for cloning tasks, and available for redistribution under GPL2.0.Genbeans - Includes manipulation of FASTA files in a GUI.SeqKit - nice tools for manipulating FASTA/FASTQ filesAdded in BIRCH 3.40.TBTools - A Java application with a diverse set of genomics functions.Omics Playground - Web based system for analysis of omics data.15.1 Maybe its time to phase out Phylip.13.1 Basic Restriction Enzyme Tasks in BioLegato.7 Gene Expression/Transcriptome Analysis.3.3 Assembly viewers and Quality Assessment.3.1.4 Removel of non-paired reads from paired files.3.1.2 Trimming, elimination of small fragments etc.