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Task: Next Generation Sequencing
Metapackage: false
Description: Debian Med bioinformatics applications usable in Next Generation Sequencing
It aims at gettting packages which specializes in alignment of
sequences produced by next generation sequencing.
Comment: Do not build a metapackage because it is not clear in how far this set of
packages is complete regarding NGS.
Depends:
bedtools,
bwa,
bowtie,
fastx-toolkit,
filo,
last-align,
maq,
picard-tools,
r-bioc-edger,
r-bioc-hilbertvis,
samtools,
sra-toolkit,
ssake,
tabix,
tophat,
vcftools,
velvet
Depends: mothur
Depends: qiime
Depends: cufflinks
Depends: mira-assembler
X-Mark: Prospective packages are starting here.
Depends: kissplice
X-Mark: Packages in Vcs - Information about these is queried from UDD as well
Depends: mosaik-aligner
Depends: forge
Homepage: http://combiol.org/forge/
License: Apache 2.0
Pkg-Description: genome assembler for mixed read types
Forge Genome Assembler is a parallel, MPI based genome assembler for
mixed read types.
.
Forge is a classic "Overlap layout consensus" genome assembler written
by Darren Platt and Dirk Evers. Implemented in C++ and using the
parallel MPI library, it runs on one or more machines in a network and
can scale to very large numbers of reads provided there is enough
collective memory on the machines used. It generates a full consensus
alignment of all reads, can handle mixtures of sanger, 454 and illumina
reads. There is some support for solid color space and it includes built
in tools for vector trimming and contamination screening.
.
Forge and was originally developed at Exelixis and they have kindly
agreed to place the software which underwent much subsequent development
outside Exelixis, into the public domain. Forge works with most of the
common MPI implementations.
Remark: Competitor to MIRA2 and wgs-assembler
This package was requested by William Spooner <whs@eaglegenomics.com> as
a competitor to MIRA2 and wgs-assembler.
Depends: uc-echo
Depends: annovar
Homepage: http://www.openbioinformatics.org/annovar/
License: Open Source for non-profit
Pkg-Description: annotate genetic variants detected from diverse genomes
ANNOVAR is an efficient software tool to utilize update-to-date information
to functionally annotate genetic variants detected from diverse genomes
(including human genome hg18, hg19, as well as mouse, worm, fly, yeast and
many others). Given a list of variants with chromosome, start position, end
position, reference nucleotide and observed nucleotides, ANNOVAR can perform:
.
1. Gene-based annotation: identify whether SNPs or CNVs cause protein coding
changes and the amino acids that are affected. Users can flexibly use RefSeq
genes, UCSC genes, ENSEMBL genes, GENCODE genes, or many other gene definition
systems.
2. Region-based annotations: identify variants in specific genomic regions,
for example, conserved regions among 44 species, predicted transcription
factor binding sites, segmental duplication regions, GWAS hits, database
of genomic variants, DNAse I hypersensitivity sites, ENCODE
H3K4Me1/H3K4Me3/H3K27Ac/CTCF sites, ChIP-Seq peaks, RNA-Seq peaks, or many
other annotations on genomic intervals.
3. Filter-based annotation: identify variants that are reported in dbSNP,
or identify the subset of common SNPs (MAF>1%) in the 1000 Genome Project,
or identify subset of non-synonymous SNPs with SIFT score>0.05, or many
other annotations on specific mutations.
4. Other functionalities: Retrieve the nucleotide sequence in any
user-specific genomic positions in batch, identify a candidate gene list
for Mendelian diseases from exome data, identify a list of SNPs from
1000 Genomes that are in strong LD with a GWAS hit, and many other
creative utilities.
.
In a modern desktop computer (3GHz Intel Xeon CPU, 8Gb memory), for
4.7 million variants, ANNOVAR requires ~4 minutes to perform
gene-based functional annotation, or ~15 minutes to perform stepwise
"variants reduction" procedure, making it practical to handle hundreds
of human genomes in a day.
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