[Bio-linux-list] Sickle biolinux 8
Flavia Flaviani
flacchy at gmail.com
Sat Jun 11 06:59:08 EDT 2016
Hi Tony,
thank you for your advice. I have run all your adviced commnads
:~$ apt search sickle
Sorting... Done
Full Text Search... Done
r-cran-phtt/trusty 3.1.2-1cran1ppa0trusty0 all
GNU R package "Panel Data Analysis with Heterogeneous Time
sickle/trusty 1.33-1biolinux1 amd64
windowed adaptive trimming tool for FASTQ files using quality
flafla at biolinux:~$
flafla at biolinux:~$ apt show sickle
Package: sickle
Priority: optional
Section: science
Installed-Size: 74.8 kB
Maintainer: Debian Med Packaging Team <
debian-med-packaging at lists.alioth.debian.org>
Version: 1.33-1biolinux1
Depends: libc6 (>= 2.14), zlib1g (>= 1:1.1.4)
Download-Size: 17.3 kB
APT-Sources: http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main
amd64 Packages
Description: windowed adaptive trimming tool for FASTQ files using quality
Most modern sequencing technologies produce reads that have deteriorating
quality towards the 3'-end. Incorrectly called bases here negatively
impact assembles, mapping, and downstream bioinformatics analyses.
.
Sickle is a tool that uses sliding windows along with quality and length
thresholds to determine when quality is sufficiently low to trim the
3'-end of reads. It will also discard reads based upon the length
threshold. It takes the quality values and slides a window across them
whose length is 0.1 times the length of the read. If this length is less
than 1, then the window is set to be equal to the length of the read.
Otherwise, the window slides along the quality values until the average
quality in the window drops below the threshold. At that point the
algorithm determines where in the window the drop occurs and cuts both the
read and quality strings there. However, if the cut point is less than the
minimum length threshold, then the read is discarded entirely.
.
Sickle supports four types of quality values: Illumina, Solexa, Phred,
and Sanger. Note that the Solexa quality setting is an approximation (the
actual conversion is a non-linear transformation). The end approximation
is close.
.
Sickle also supports gzipped file inputs.
BUT in the last command I get this :
~$ apt-cache policy sickle
sickle:
Installed: (none)
Candidate: 1.33-1biolinux1
Version table:
1.33-1biolinux1 0
500 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main
amd64 Packages
So it seems that it's there but not installed. Can you advise me on how to
fix this?
thank you so much in advance,
Regards
Flavia
2016-06-10 18:24 GMT+01:00 Tony Travis <tony.travis at minke-informatics.co.uk>
:
> On 10/06/16 17:07, Flavia Flaviani wrote:
> > Hi everyone,
> >
> > I have been asked to installed sickle on our biolinux machine and before
> > installing something that was already installed I've visited the
> > biolinux page http://environmentalomics.org/bio-linux-software-list/
> >
> > Here I can see that sicke should be available directly in biolinux:
> >
> >
> > sickle 1.33 windowed adaptive trimming tool for FASTQ files
> using quality
> >
> >
> > When we type in the terminal sickle we get the message :"No command
> > 'sickle' found, "
> >
> >
> >
> > so I have tried:
> >
> > $ dpkg -s sickle
> >
> >
> > and I got this message:
> >
> > $dpkg-query: package 'sickle' is not installed and no information is
> > available
> > Use dpkg --info (= dpkg-deb --info) to examine archive files,
> > and dpkg --contents (= dpkg-deb --contents) to list their contents.
> >
> >
> > Would you advise me to install the program from github or is there
> > something I am missing for which I cannot access the preinstalled one?
>
> Hi, Flavia.
>
> You should only use "dpkg" for low-level tasks when you really have to.
> For example to fix things that are broken and for installing downloaded
> .deb packages manually (although "gdebi" is easier to use). You would be
> better using the high-level "apt" command instead. First update the
> "apt" database:
>
> > root at wildcat:~# apt update
> > Ign http://extras.ubuntu.com trusty InRelease
> > Ign http://archive.ubuntu.com precise InRelease
> > [...]
>
> Then search for e.g. the "sickle" package in the repositories:
>
> > root at wildcat:~# apt search sickle
> > Sorting... Done
> > Full Text Search... Done
> > r-cran-phtt/trusty 3.1.2-1cran1ppa0trusty0 all
> > GNU R package "Panel Data Analysis with Heterogeneous Time
> >
> > sickle/trusty,now 1.33-1biolinux1 amd64 [installed]
> > windowed adaptive trimming tool for FASTQ files using quality
>
> Having found that there is, indeed, a "sickle" package, you can show
> details about the package and its dependencies:
>
> > root at wildcat:~# apt show sickle
> > Package: sickle
> > Priority: optional
> > Section: science
> > Installed-Size: 74.8 kB
> > Maintainer: Debian Med Packaging Team <
> debian-med-packaging at lists.alioth.debian.org>
> > Version: 1.33-1biolinux1
> > Depends: libc6 (>= 2.14), zlib1g (>= 1:1.1.4)
> > Download-Size: 17.3 kB
> > APT-Manual-Installed: yes
> > APT-Sources: http://ppa.launchpad.net/nebc/bio-linux/ubuntu/
> trusty/main amd64 Packages
> > Description: windowed adaptive trimming tool for FASTQ files using
> quality
> > Most modern sequencing technologies produce reads that have
> deteriorating
> > quality towards the 3'-end. Incorrectly called bases here negatively
> impact
> > assembles, mapping, and downstream bioinformatics analyses.
> > .
> > Sickle is a tool that uses sliding windows along with quality and length
> > thresholds to determine when quality is sufficiently low to trim the
> 3'-end
> > of reads. It will also discard reads based upon the length threshold.
> It takes
> > the quality values and slides a window across them whose length is 0.1
> times
> > the length of the read. If this length is less than 1, then the window
> is set
> > to be equal to the length of the read. Otherwise, the window slides
> along the
> > quality values until the average quality in the window drops below the
> > threshold. At that point the algorithm determines where in the window
> the drop
> > occurs and cuts both the read and quality strings there. However, if
> the cut
> > point is less than the minimum length threshold, then the read is
> discarded
> > entirely.
> > .
> > Sickle supports four types of quality values: Illumina, Solexa, Phred,
> and
> > Sanger. Note that the Solexa quality setting is an approximation (the
> actual
> > conversion is a non-linear transformation). The end approximation is
> close.
> > .
> > Sickle also supports gzipped file inputs.
>
> You can also see if other versions or upgrade candidates are available:
>
> > root at wildcat:~# apt-cache policy sickle
> > sickle:
> > Installed: 1.33-1biolinux1
> > Candidate: 1.33-1biolinux1
> > Version table:
> > *** 1.33-1biolinux1 0
> > 500 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main
> amd64 Packages
> > 100 /var/lib/dpkg/status
>
> HTH,
>
> Tony.
>
> --
> Minke Informatics Limited, Registered in Scotland - Company No. SC419028
> Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
> tel. +44(0)19755 63548 http://minke-informatics.co.uk
> mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk
> _______________________________________________
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>
--
Flavia Flaviani
*PhD student*
Department of Molecular and Cell Biology
University of Cape Town, South Africa
In collaboration with
The marine Biological Association of the UK (Plymouth, UK)
flvfla001 at myuct.ac.za
flafla at mba.ac.uk
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