Important bioinformatics tools for analysis of NGS data
A forum for next generation sequencing, almost everything about NGS are included.
SEQanswers
https://seqanswers.com/
Useful tools in NGS are listed here:
https://seqanswers.com/wiki/Software/list
Some tools are summarized in this paper:
Next-generation sequencing technologies and their implications for crop genetics and breeding
Trends in Biotechnology
Volume 27, Issue 9, September 2009, Pages 522-530
Bowtie and MAQ are my favorites, as the former is "ultra fast", The later includes most functions.
SOAP was writtern by BGI.
Alignment, assembly and visualization tools
Velvet (https://www.ebi.ac.uk/~zerbino/velvet/): tool for de novo
assembly of short and paired reads [70].
EULER (https://euler-assembler.ucsd.edu/portal/): tool to generate
short-read assembly and facilitate assembly of combined reads of
NGS and Sanger sequencing [71].
GMAP (https://www.gene.com/share/gmap/): program to map and
align cDNA sequences to genome sequence using minimal time and
memory, facilitates batch processing [72].
MOSAIK (https://bioinformatics.bc.edu/marthlab/Mosaik): tool for
pairwise alignment of NGS data to reference sequences.
RMAP (https://rulai.cshl.edu/rmap/): tool to align short reads to a
reference genome [30].
SHARCGS (https://sharcgs.molgen.mpg.de/): tool for de novo assembly
of short reads [73].
SOAP (https://soap.genomics.org.cn/): program for gapped and
ungapped alignment of short reads to reference sequences, facilitates
single or pair-end resequencing, smRNA discovery and mRNA tag
sequence mapping [74].
VCAKE (https://sourceforge.net/projects/vcake): tool for de novo
assembly of short reads with robust error detection [75].
Zoom (https://www.bioinformaticssolutions.com/products/zoom/index.
php): tool to map millions of short reads to reference genomes
and carry out post-analysis [76].
EagleView (https://bioinformatics.bc.edu/marthlab/EagleView): display
tool for visually inspecting the quality of genome assembly and
validating polymorphism candidate sites [77].
JMP1 Genomics (https://www.jmp.com/software/genomics/): tool
for NGS data visualization and statistical analysis from SAS.
Sequence variant discovery tools
SNPsniffer (https://bioinformatics.bc.edu/marthlab/Polymorphism_
Discovery_in_Next-Generation_Sequence_Data): tool for SNP discovery
specifically designed for Roche/454 sequences.
Atlas-SNP (https://code.google.com/p/atlas-snp/): tool for SNP and
indel discovery from genome resequencing using NGS technologies
[78].
SeqMap (https://biogibbs.stanford.edu/~jiangh/SeqMap/): tool to
map short sequences to a reference genome and detect multiple
substitutions and indels [79].
ssahaSNP (https://www.sanger.ac.uk/Software/analysis/ssahaSNP/):
tool to detect homozygous SNPs and indels.
Integrated tools
AlpheusTM (https://alpheus.ncgr.org/): web-based cyber infrastructure
platform for pipelining, visualization and analysis of gigabase-scale
NGS data and internet-accessible software for variant discovery and
isoform identification [31].
MAQ (https://maq.sourceforge.net/): program for mapping and
assembly of short reads. It can also report SNPs and indels using a
simple assembly visualizer (Maqview) [80].
NextGENeTM (https://www.softgenetics.com/NextGENe.html): software
to analyze NGS data for de novo assembly, SNP and indel
detection and transcriptome analysis.
SeqMan genome analyzer (https://www.dnastar.com/products/SMGA.php)
: software with capacity to align NGS and Sanger data
and detect SNPs; also facilitates visualization.
CLCbio Genomics Workbench (https://www.clcbio.com): tool for de
novo and reference assembly of Sanger and NGS sequence data, SNP
detection and browsing.
PanGEA (https://www.kofler.or.at/Bioinformatics/PanGEA/index.html):
tool to map NGS data to whole genomes, with SNP
detection and display capabilities [81].
Review Trends in Biotechnology Vol.27 No.9
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