<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/39329?offset=20 https://bioinformaticsonline.com/bookmarks/view/37561/hercules-a-profile-hmm-based-hybrid-error-correction-algorithm-for-long-reads Mon, 20 Aug 2018 14:14:11 -0500 https://bioinformaticsonline.com/bookmarks/view/37561/hercules-a-profile-hmm-based-hybrid-error-correction-algorithm-for-long-reads <![CDATA[Hercules: a profile HMM-based hybrid error correction algorithm for long reads]]> Choosing whether to use second or third generation sequencing platforms can lead to trade-offs between accuracy and read length. Several studies require long and accurate reads including de novo assembly, fusion and structural variation detection. In such cases researchers often combine both technologies and the more erroneous long reads are corrected using the short reads. Current approaches rely on various graph based alignment techniques and do not take the error profile of the underlying technology into account. Memory- and time- efficient machine learning algorithms that address these shortcomings have the potential to achieve better and more accurate integration of these two technologies. Results: We designed and developed Hercules, the first machine learning-based long read error correction algorithm. The algorithm models every long read as a profile Hidden Markov Model with respect to the underlying platformtextquoterights error profile. The algorithm learns a posterior transition/emission probability distribution for each long read and uses this to correct errors in these reads. Using datasets from two DNA-seq BAC clones (CH17-157L1 and CH17-227A2), and human brain cerebellum polyA RNA-seq, we show that Hercules-corrected reads have the highest mapping rate among all competing algorithms and highest accuracy when most of the basepairs of a long read are covered with short reads. Availability:

Hercules source code is available at https://github.com/BilkentCompGen/Hercules

Address of the bookmark: https://github.com/BilkentCompGen/Hercules

]]> Jit https://bioinformaticsonline.com/file/view/2780/life-of-bi Thu, 22 Aug 2013 16:13:36 -0500 https://bioinformaticsonline.com/file/view/2780/life-of-bi <![CDATA[Life of BI !!!]]> Hmm .. Don't worry you read it right .. this is not pi but bi ... "life of Bioinformatician(BI)". 

Disclaimer: This cartoon is solely designed to create humour and fun, not to offend any PI, supervisor or student.

]]> Jitendra Narayan https://bioinformaticsonline.com/file/view/3952/ancestor-at-work Sun, 25 Aug 2013 19:45:28 -0500 https://bioinformaticsonline.com/file/view/3952/ancestor-at-work <![CDATA[Ancestor at work !!!]]> When they will learn Bioinformatics :)

]]> Jit https://bioinformaticsonline.com/file/view/5719/bioinformatician-kidnaped Thu, 17 Oct 2013 05:10:23 -0500 https://bioinformaticsonline.com/file/view/5719/bioinformatician-kidnaped <![CDATA[Bioinformatician kidnaped !!!]]> Some fish kidnaped a bioinformatician for their genome analysis.

]]> Rahul Nayak https://bioinformaticsonline.com/file/view/8650/bioinformatician-duties-and-jobs Wed, 05 Mar 2014 14:32:26 -0600 https://bioinformaticsonline.com/file/view/8650/bioinformatician-duties-and-jobs <![CDATA[Bioinformatician duties and jobs !!!]]> Needle in a haystack ... ohh yes this is what bioinformatician do. We handle and analyse, Terabytes and Petabytes of genomic data on daily basis.

]]> Jitendra Narayan https://bioinformaticsonline.com/file/view/10563/funny-software-engineer Fri, 09 May 2014 06:57:04 -0500 https://bioinformaticsonline.com/file/view/10563/funny-software-engineer <![CDATA[Funny software engineer]]> Ram Yash Pal https://bioinformaticsonline.com/file/view/14868/bioinformaticians-summer-vacation Wed, 03 Sep 2014 13:11:50 -0500 https://bioinformaticsonline.com/file/view/14868/bioinformaticians-summer-vacation <![CDATA[Bioinformatician's summer vacation !!!]]> Yes, the bioinformatician do spend their summer vacation like this. They spend more time on cheking the JOBS running on various servers.

]]> Jit https://bioinformaticsonline.com/fun/view/23959/bioinformatics-jokes Fri, 21 Aug 2015 01:26:54 -0500 https://bioinformaticsonline.com/fun/view/23959/bioinformatics-jokes <![CDATA[Bioinformatics Jokes !!]]> Why was the Bioinformatics fired from his job?

A: He was getting too Sassy.

 

What did the bioinformatician say when he found out his team stopped using version control?

A: Y’all better Git!

 

Why did the computational biologist stay home from work?

A: He had a code!

 

Why was the bioinformatician's paper was rejected?

A: Journal thought it seemed scripted.

 

How can you tell that a Bioinformatics is working?

A: You can hear him Grunting!

 

Why bioinformatician always silence?

A: Because bioinformatician calmly whisper, “SSH”

 

Why was the bioinformatician always so sleepy?

A: He/She wasn’t given any Java.

 

Why did the program/software hanged?

A: Because genome float.

 

Why was the class upset that its parent died?

A: Because it wouldn’t be getting the inheritance!

 

Why did bioinformatician always works on the command line?

A: Because they don't want to scare you with huge amount of data!

 

Why did the bioinformatician attend the gay pride parade?

A: They supported polymorphism.

 

Why did bioinformatician prefer awk, PerlOneliner?

A: Because even computer can't handle to load the data.

 

Why don’t bioinformatician get along with others?

A: They’re too MEAN.

 

Why computational biologist are cool?

A: Because they are scripted!!

 

Why they talk $ unzip; strip; touch; finger; grep; mount; fsck; more; yes; fsck; fsck; umount; clean; sleep;

A: Ah, Ohhh, dude, these are *NIX commands

 

Did they really hack genome?

A: Yes, I guess so.

]]> Jitendra Prajapati https://bioinformaticsonline.com/file/view/38029/biologist-versus-computational-biologist Mon, 29 Oct 2018 04:23:24 -0500 https://bioinformaticsonline.com/file/view/38029/biologist-versus-computational-biologist <![CDATA[Biologist versus computational biologist !]]> This is how it work :)

]]> Abhimanyu Singh https://bioinformaticsonline.com/pages/view/36497/installing-python-numpy Mon, 07 May 2018 04:31:25 -0500 https://bioinformaticsonline.com/pages/view/36497/installing-python-numpy <![CDATA[Installing python-numpy !]]> $ sudo apt-get install python-numpy python-scipy python-matplotlib ipython ipython-notebook python-pandas python-sympy python-nose
[sudo] password for urbe:
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages were automatically installed and are no longer required:
bridge-utils containerd linux-headers-4.4.0-116 linux-headers-4.4.0-116-generic linux-headers-4.4.0-21 linux-headers-4.4.0-21-generic
linux-image-4.4.0-116-generic linux-image-4.4.0-21-generic linux-image-extra-4.4.0-116-generic linux-image-extra-4.4.0-21-generic
linux-signed-image-4.4.0-116-generic runc ubuntu-fan
Use 'sudo apt autoremove' to remove them.
The following additional packages will be installed:
blt fonts-lyx fonts-mathjax ipython-notebook-common isympy libaec0 libamd2.4.1 libdsdp-5.8gf libglpk36 libgsl2 libhdf5-10 libjs-highlight
libjs-highlight.js libjs-jquery-ui libjs-marked libjs-mathjax libjs-underscore libsz2 python-antlr python-bs4 python-chardet python-cvxopt
python-cycler python-dateutil python-decorator python-glade2 python-gmpy python-html5lib python-imaging python-jdcal python-jinja2 python-joblib
python-lxml python-markupsafe python-matplotlib-data python-mpmath python-numexpr python-openpyxl python-pandas-lib python-patsy python-pexpect
python-pil python-ptyprocess python-py python-pycurl python-pyglet python-pymysql python-pyparsing python-pytest python-simplegeneric
python-simplejson python-statsmodels python-statsmodels-lib python-sympy-doc python-tables python-tables-data python-tables-lib python-tk
python-tornado python-tz python-xlrd python-xlwt python-zmq tk8.6-blt2.5 ttf-bitstream-vera
Suggested packages:
blt-demo ipython-doc ipython-qtconsole python-pygments nodejs pandoc libiodbc2-dev libmysqlclient-dev gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info
| gsl-ref-html libjs-jquery-ui-docs fonts-mathjax-extras libjs-mathjax-doc python-gtk2-doc python-genshi python-jinja2-doc python-lxml-dbg
python-lxml-doc ffmpeg inkscape python-cairocffi python-configobj python-excelerator python-matplotlib-doc python-qt4 python-sip python-traits
python-wxgtk3.0 ttf-staypuft python-gmpy2 python-mpmath-doc python-coverage python-nose-doc python-numpy-dbg python-numpy-doc python-pandas-doc
python-patsy-doc python-pexpect-doc python-pil-doc python-pil-dbg subversion python-pytest-xdist libcurl4-gnutls-dev python-pycurl-dbg
python-pycurl-doc python-pymysql-doc python-mock python-scipy-doc python-statsmodels-doc python-tables-doc python-netcdf vitables tix
python-tk-dbg
The following NEW packages will be installed:
blt fonts-lyx fonts-mathjax ipython ipython-notebook ipython-notebook-common isympy libaec0 libamd2.4.1 libdsdp-5.8gf libglpk36 libgsl2
libhdf5-10 libjs-highlight libjs-highlight.js libjs-jquery-ui libjs-marked libjs-mathjax libjs-underscore libsz2 python-antlr python-bs4
python-chardet python-cvxopt python-cycler python-dateutil python-decorator python-glade2 python-gmpy python-html5lib python-imaging
python-jdcal python-jinja2 python-joblib python-lxml python-markupsafe python-matplotlib python-matplotlib-data python-mpmath python-nose
python-numexpr python-numpy python-openpyxl python-pandas python-pandas-lib python-patsy python-pexpect python-pil python-ptyprocess python-py
python-pycurl python-pyglet python-pymysql python-pyparsing python-pytest python-scipy python-simplegeneric python-simplejson python-statsmodels
python-statsmodels-lib python-sympy python-sympy-doc python-tables python-tables-data python-tables-lib python-tk python-tornado python-tz
python-xlrd python-xlwt python-zmq tk8.6-blt2.5 ttf-bitstream-vera
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➜ redundans git:(master) ✗ python2 redundans.py -v -i test/*_?.fq.gz -f test/contigs.fa -o test/run1
Options: Namespace(fasta='test/contigs.fa', fastq=['test/5000_1.fq.gz', 'test/5000_2.fq.gz', 'test/600_1.fq.gz', 'test/600_2.fq.gz'], identity=0.51, iters=2, joins=5, limit=0.2, linkratio=0.7, log=', mode 'w' at 0x7f85d1de31e0>, longreads=[], mapq=10, mem=16, minLength=200, nocleaning=True, nogapclosing=True, norearrangements=False, noreduction=True, noscaffolding=True, outdir='test/run1', overlap=0.8, reference='', resume=False, threads=4, tmp='/tmp', usebwa=False, verbose=True)

##################################################
[Mon May 7 11:29:18 2018] Reduction...
#file name genome size contigs heterozygous size [%] heterozygous contigs [%] identity [%] possible joins homozygous size [%] homozygous contigs [%]
/usr/lib/python2.7/dist-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.
warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.')
test/run1/contigs.fa 163897 245 66377 40.50 221 90.20 94.854 0 97520 59.50 24 9.80

##################################################
[Mon May 7 11:29:29 2018] Estimating parameters of libraries...
Aligning 19504 mates per library...
Insert size statistics Mates orientation stats
FastQ files read length median mean stdev FF FR RF RR
test/5000_1.fq.gz test/5000_2.fq.gz 50 4998 4990.20 721.47 0 4674 0 0
test/600_1.fq.gz test/600_2.fq.gz 100 599 598.63 47.68 0 10000 0 0

##################################################
[Mon May 7 11:29:29 2018] Scaffolding...
iteration 1.1: test/run1/contigs.reduced.fa 24 97520 39.355 17 94157 7321 2195 0 29603
19505 pairs. 17302 passed filtering [88.71%]. 1627 in different contigs [8.34%].
1526 pairs. 558 in different contigs [36.57%].
iteration 1.2: test/run1/_sspace.1.1.fa 3 97626 39.344 3 97626 87536 6063 821 87536
19505 pairs. 17607 passed filtering [90.27%]. 182 in different contigs [0.93%].
1077 pairs. 124 in different contigs [11.51%].
iteration 2.1: test/run1/_sspace.1.2.fa 3 97626 39.344 3 97626 87536 6063 821 87536
19505 pairs. 15112 passed filtering [77.48%]. 1295 in different contigs [6.64%].
3417 pairs. 396 in different contigs [11.59%].
iteration 2.2: test/run1/_sspace.2.1.fa 1 99133 39.344 1 99133 99133 99133 2328 99133
19505 pairs. 15152 passed filtering [77.68%]. 0 in different contigs [0.00%].
3398 pairs. 0 in different contigs [0.00%].

##################################################
[Mon May 7 11:29:34 2018] Gap closing...
iteration 1.1: test/run1/scaffolds.fa 1 99133 39.344 1 99133 99133 99133 2328 99133

##################################################
[Mon May 7 11:29:35 2018] Final reduction...
#file name genome size contigs heterozygous size [%] heterozygous contigs [%] identity [%] possible joins homozygous size [%] homozygous contigs [%]
[WARNING] Nothing reduced!
test/run1/scaffolds.filled.fa 99390 1 0 0.00 0 0.00 0.000 0 99390 100.00 1 100.00

##################################################
[Mon May 7 11:29:35 2018] Reporting statistics...
#fname contigs bases GC [%] contigs >1kb bases in contigs >1kb N50 N90 Ns longest
test/contigs.fa 245 163897 40.298 24 117391 3975 233 0 29603
test/run1/contigs.fa 245 163897 40.298 24 117391 3975 233 0 29603
test/run1/contigs.reduced.fa 24 97520 39.355 17 94157 7321 2195 0 29603
test/run1/_sspace.1.1.fa 3 97626 39.344 3 97626 87536 6063 821 87536
test/run1/_sspace.1.2.fa 3 97626 39.344 3 97626 87536 6063 821 87536
test/run1/_sspace.2.1.fa 1 99133 39.344 1 99133 99133 99133 2328 99133
test/run1/_sspace.2.2.fa 1 99133 39.344 1 99133 99133 99133 2328 99133
test/run1/scaffolds.fa 1 99133 39.344 1 99133 99133 99133 2328 99133
test/run1/_gapcloser.1.1.fa 1 99390 39.689 1 99390 99390 99390 2 99390
test/run1/scaffolds.filled.fa 1 99390 39.689 1 99390 99390 99390 2 99390
test/run1/scaffolds.reduced.fa 1 99390 39.689 1 99390 99390 99390 2 99390

##################################################
[Mon May 7 11:29:35 2018] Cleaning-up...
#Time elapsed: 0:00:17.376924

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