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Literature DB >> 19129211

SCARF: maximizing next-generation EST assemblies for evolutionary and population genomic analyses.

Michael S Barker¹, Katrina M Dlugosch, A Chaitanya C Reddy, Sarah N Amyotte, Loren H Rieseberg.

Abstract

SUMMARY: Scaffolded and Corrected Assembly of Roche 454 (SCARF) is a next-generation sequence assembly tool for evolutionary genomics that is designed especially for assembling 454 EST sequences against high-quality reference sequences from related species. The program was created to knit together 454 contigs that do not assemble during traditional de novo assembly, using a reference sequence library to orient the 454 sequences. AVAILABILITY: SCARF is freely available at http://msbarker.com/software.htm, and is released under the open source GPLv3 license (http://www.opensource.org/licenses/gpl-3.0.html.

Entities: Disease

Mesh：

Year: 2009 PMID： 19129211 DOI： 10.1093/bioinformatics/btp011

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

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Cited

9 in total

Review 1. Community genetics: what have we accomplished and where should we be going?

Authors: Erika I Hersch-Green; Nash E Turley; Marc T J Johnson
Journal: Philos Trans R Soc Lond B Biol Sci Date: 2011-05-12 Impact factor: 6.237

2. EvoPipes.net: Bioinformatic Tools for Ecological and Evolutionary Genomics.

Authors: Michael S Barker; Katrina M Dlugosch; Louie Dinh; R Sashikiran Challa; Nolan C Kane; Matthew G King; Loren H Rieseberg
Journal: Evol Bioinform Online Date: 2010-10-20 Impact factor: 1.625

3. Allele discovery of ten candidate drought-response genes in Austrian oak using a systematically informatics approach based on 454 amplicon sequencing.

Authors: Andreas Homolka; Thomas Eder; Dieter Kopecky; Maria Berenyi; Kornel Burg; Silvia Fluch
Journal: BMC Res Notes Date: 2012-04-03

4. Comparative metagenomic analysis of soil microbial communities across three hexachlorocyclohexane contamination levels.

Authors: Naseer Sangwan; Pushp Lata; Vatsala Dwivedi; Amit Singh; Neha Niharika; Jasvinder Kaur; Shailly Anand; Jaya Malhotra; Swati Jindal; Aeshna Nigam; Devi Lal; Ankita Dua; Anjali Saxena; Nidhi Garg; Mansi Verma; Jaspreet Kaur; Udita Mukherjee; Jack A Gilbert; Scot E Dowd; Rajagopal Raman; Paramjit Khurana; Jitendra P Khurana; Rup Lal
Journal: PLoS One Date: 2012-09-28 Impact factor: 3.240

SCARF: maximizing next-generation EST assemblies for evolutionary and population genomic analyses.

Review 1. Community genetics: what have we accomplished and where should we be going?

2. EvoPipes.net: Bioinformatic Tools for Ecological and Evolutionary Genomics.

3. Allele discovery of ten candidate drought-response genes in Austrian oak using a systematically informatics approach based on 454 amplicon sequencing.

4. Comparative metagenomic analysis of soil microbial communities across three hexachlorocyclohexane contamination levels.

5. Next generation sequencing and analysis of a conserved transcriptome of New Zealand's kiwi.

6. Gene discovery in the horned beetle Onthophagus taurus.

7. Comparing de novo assemblers for 454 transcriptome data.

8. CAPRG: sequence assembling pipeline for next generation sequencing of non-model organisms.

9. A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation.