User: oxfordsoccer

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oxfordsoccer10
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Posts by oxfordsoccer

<prev • 9 results • page 1 of 1 • next >
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(Closed) How to set FASTQ trimming parameters before de novo assembly of the birch chloroplast genome?
... How to set FASTQ trimming parameters before de novo assembly of the birch chloroplast genome? How much to cut and filter? On what facts to rely on? And is it obligatory to scaffold the resultant contigs and remove gaps before putting contig to the annotation engine? ...
plant trimming fastq denovo assembly written 2.8 years ago by oxfordsoccer10
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(Closed) What software is proper for the reference guided de novo assmebly and annotation of the Betula birch chloroplast genome?
... What software is proper for the reference guided de novo assmebly and annotation of the Betula birch chloroplast genome? We have tried BBMap, MIRA, NextGene, however subsequent annotation with Prokka is not complete. ...
birch assembly plant denovo annotation written 2.8 years ago by oxfordsoccer10
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Comment: C: Where to download a human exome reference file for Illumina FASTQs TruKit data a
... Where to download it in Genbank format? Thank you I have found ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/ Is it correct? ...
written 2.8 years ago by oxfordsoccer10
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(Closed) Where to download a human exome reference file for Illumina FASTQs TruKit data alignment?
... Where to download a human exome reference file for Illumina FASTQs TruKit data alignment? Thx. ...
exome illumina alignment reference human written 2.8 years ago by oxfordsoccer10
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Is there any alternative to QUAST software to evaluate de novo assembly results?
... Is there any alternative to QUAST software to evaluate de novo assembly results? I need to check a set/batch of de novo assembled plant contigs to compare data quality of the data computed with various algorithms and chosen k-mers. Thank you. ...
assembly quality evaluation quast written 2.8 years ago by oxfordsoccer10 • updated 2.8 years ago by Sej Modha4.7k
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What software to choose to do reference-assisted Birch Betula chloroplast genome assembly and subsequent annotation?
... What software to choose to do reference-assisted Birch Betula chloroplast genome assembly and subsequent annotation? I have tried de novo assembly using BBMap, NextGene`s DeBrujin with various k-mers, Flotton and PE Flotton, then run Prokka and RAST on the resultant contigs. Did not apply scaffold ...
de novo assembly tree plant written 2.8 years ago by oxfordsoccer10
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What genome assembler to choose for an unpaired FASTQ data derived from a Birch chloroplast?
... What genome assembler to choose for an unpaired FASTQ data derived from a Birch chloroplast? And other tools for pre- and post-processing also File type Conventional base calls Encoding Sanger / Illumina 1.9 (actually Ion Torrent data) Total Sequences 376768 Sequences flagged as poor quality 0 ...
chloroplast assembly fastq birch plant written 2.8 years ago by oxfordsoccer10 • updated 2.8 years ago by Asaf8.5k
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How to run SNPEff jar for a batch of VCF files using GNU parallel tool?
... How to run SNPEff jar for a batch of VCF files (300 items) using GNU parallel tool? Need a code example. Found only one example somehow similar to my question https://stackoverflow.com/questions/28072857/s-gnu-parallel-execution-of-commands-from-file-few-at-a-time. Thx. ...
software variant calling snpeff gnu parallel bash written 2.8 years ago by oxfordsoccer10
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(Closed) What international organizations provide grant competition for NGS microbial research conducted in Russia and Belarus?
... What international organizations provide grant competition for NGS microbial research conducted in Russia and Belarus? I am looking for collaborators and opportunities to find support for NGS microbial research and relevant software development. ...
ngs grant research project written 2.8 years ago by oxfordsoccer10

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