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Home > A Comprehensive Study of De Novo Genome Assemblers: Current Challenges and Future Prospective

A Comprehensive Study of De Novo Genome Assemblers: Current Challenges and Future Prospective

Thesis Info

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External Link

Author

Abdul Rafay Khan

Institute

Virtual University of Pakistan

Institute Type

Public

City

Lahore

Province

Punjab

Country

Pakistan

Thesis Completing Year

2016

Thesis Completion Status

Completed

Subject

Software Engineering

Language

English

Link

http://vspace.vu.edu.pk/detail.aspx?id=114

Added

2021-02-17 19:49:13

Modified

2024-03-24 20:25:49

ARI ID

1676720970222

Similar


Current advancements in next generation sequencing technology have made possible to sequence whole genome but assembling a large number of short reads is still a big challenge. In this article, we present the comparative study of seven assemblers namely ABySS, Velvet, Edena, SGA, Ray, SSAKE and Perga, using seven paired-end and eight single-end prokaryotic datasets from Illumina platform. Results showed that in case of single-end datasets, Velvet and ABySS outperformed all seven assemblers with comparatively low assembling time and high genome fraction. The Velvet consumed the least amount of memory than any other assembler. In case of paired-end datasets, Velvet consumed least amount of time and produced high genome fraction after ABySS and Ray. In term of low memory usage, SGA and Edena outperformed all seven assemblers. The Ray also showed good genome fraction, however extremely high assembling time consumed by the Ray might make it prohibitively slow on larger datasets of single and paired-end data. Our study would provide assistance to the biologists and bioinformaticians for selecting the suitable assembler according to their datasets. This will also help the developers to upgrade or develop a new assembler for de novo assembling.
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عدلیہ دا انصاف

عدلیہ د اانصاف
سیشن جج بہاولنگر دا مہر محمد عارف سیال
مظلوماں تے بے کساں دا کردا ہے بہت خیال
مظلوماں دی داد رسی لئی جدوں آپ عدالت آندے
سن فریاد قانون مطابق حکم صادر فرماندے
چھیتی عدل ملن تے سائل خوشیاں پاندے
جسٹس محمد منیر مغل دے نے آپ ہم خیال
پاک پاکیزہ رہن دا شوق زیادہ نیکاں صحبت پائی
من پاک تن وی صاف تے ماحول دی چاہن صفائی
عزت عظمت رب نے دتی بہتی شہرت پائی
ہر دم رکھدے یاد اللہ نوں کردے صدق مقال
کرن ہدایت ججز تائیں عدل نوں اپنانا
عدل انصاف قائم کرکے عدلیہ دی شان ودھانا
چنگی شہرت چنگی ہوندی چنگا کردکھانا
شعبہ عدل دا ہے در حقیقت مظلوماں دی ڈھال
بہاول نگر دی قسمت جاگی چنگا جج ہے آیا
مدت دے پرانے کیساں نوں کر سماعت نمٹایا
اہل علاقے خوشی منائی مولیٰ کرم کمایا
مظلوماں تے بے کساں دے دکھڑے دتے ٹال
سینئر سول جج چوپڑا صاحب چنگے اصولاں والے
کیساں دی گہرائی وچ جاکے فیصلے دین اوباہلے
ایہو جئے جج ہون تے کون وکیلاں نوں بھالے
نہ ہون اے جھگڑے مک جاون سب جنجال
کلم کلے رائونڈ تے نکلن کورٹاں نوں چیک کردے
کدوں آون کس ویلے آون ماتحت انہاں دے ڈردے
جام عبدالستار گسورا صاحب ہن کسے بھلے گھر دے
اوکھے سوکھے ویلے پچھن ماتحتاں دا حال
نیک نگاہ نال ہر کوئی ویکھے نیکاں نسبت پائی
اہناں دے آون پاروں ہوگئی چنگیائی
سیال صاحب دے سایہ تلے ماتحتاں موج منائی
سب ایتھے ہوگئے نے خوشحال
صوبے والے نظر عنایت توں کیوں ہوئے دور
اوتے عدلیہ تے تلے انتظامیہ گل کرن توں مجبور
چنگے لوگاں دے...

عہد نبوی میں ذرائع کے اسالیب عصر حاضر کے نوجوانوں کے لیے مشعل راہ

Since from the beginning of humanity means of communication have always been an essential need for mankind. To convey the message and to find means to communicate and express one’s thought one needs a mean to transmit the information to others. That is called communication. With the passage of time and advancement communication means also took modern shape and became advance. Islam as a complete code of life, guides humanity in the all fields of sociology, economic, politics, including mass communication. Allah the Almighty sent messengers and Prophets for the guidance of people. So they served the humanity in different periods of time in different areas. Ḥaẓrat Muḥammad (ﷺ) the last prophet of Allah used these means of communication for the prevalence and preaching of Islam, and left behind a remarkable legacy in the field of mass communication for the guidance till dooms day. Where there have been great changes in other fields and professions of life in the advanced world of contemporary era there had become a revolutionary change in the field of media. News all over the world spread in seconds. Media which is the strongest tool to approach people, but sorry to say that it is detracted badly by prevailing wrong values, vulgarity, jealousy and selfishness. There is a dire need to change the direction of noble that so (صلى الله عليه وسلم) Muhammad Prophet of methodology the towards media values like piousness, self-sacrifices, brotherhood and cooperation should be developed in people and for this purpose youth can play a pivotal and effective role in the field of mass communication. Eyes are looking towards youth of contemporary era to step forward by following our Holy contemporary the how that attempt humble a is article This. (صلى الله عليه وسلم) Prophet youth can play its role by using means of communication by taking guidance from Prophetic Era to lead media towards right direction.

Chemistry of Straw Based, Chemi-Thermo- Mechanical Pulping Black Liquor and its Chemical and Biological Treatment

Pulping of non-wood raw materials available in abundance by Kraft, soda and chemi-thermo-mechanical processes produces good quality pulp in short processing time. As these process involve less chemical doses hence the present research work was designed for the chemical recovery from the black liquors to make the waste environment friendly. In the first step of the chemical recovery of the effluents, series of experiments were conducted to determine behavior and chemistry of this straw based black liquors. Chemical composition of the chemi-thermo-mechanical pulping black liquor was determined by fractional and composite sample analysis which showed extensively low dry solids and physical and chemical properties of the black liquor tend to vary with organic to inorganic ratio of the solid contents. In the second step of the chemical recovery, desilication of the black and green liquors obtained from the chemi-thermo-mechanical pulping was conducted through the pH reduction by carbonation (80%) and sulphuric acid (85%). The green liquor sludge was found to be extremely high in COD, BOD with high reduction value. Sodium (95%) and sulphur (97%) were recovered from the sludge on dilution and addition of coagulating polymers. Second part of this thesis discusses treatment of the black liquor by chemical and/or microbiological means. In the chemical treatment process some flocculating and coagulating chemicals were employed. Addition of 200ppm alum, Buflok polymer 5425 (Buckmans) and setting of two hours yielded 82% COD reduction and solids in the range of 292ppm. Increase of alum to 1,000ppm and polymer dose of only 1ppm yielded similar results. The treatment of black liquor with hydrogen peroxide, ferric chloride, polyaluminium chloride (PAC), other 12flocculating polymers like HMW 110, HMW 130 by GEBetz and 8086 by BALCO gave no appreciable results. Activated sludge treatment was then employed to reduce the BOD of the black liquors in a series of experiments and the sludge yielded 50-60% reduction in COD, 60-65% reduction in BOD, 80-90% reduction in suspended solids and 58- 60% reduction in total solid contents. Isolation and characterization of the micro- organisms from the activated sludge was also carried out. Results showed that the degradation activity of the activated sludge was high after 12 hours and was at peak after 24 hours of aeration because enzyme activity was maximum at this stage. Finally a combination of activated sludge and chemical treatment was designed which produced reducation of 90-95% in COD, 90-95% in BOD. Suspended solids and dissolved solids were within the National Environment Quality Standard (NEQ’s) limits.