Results for "Assemble"
Blogs
CANU genome assembly parameters !
... | stands for "or". usage: canu [-correct | -trim | -assemble | -trim-assemble] \ [-s ] \...*.contigs.fasta : file containing everything that could be assembled and is part of the primary a...1933 days ago
Protocol for De novo Genome Assembly using Illumina Reads
...eanup/quality trimming. Choose an adequate parameter set for assembly. Assemble the data into scaffolds/conti...t_of_spades_assembly_all_illumina A significant range of short-read assemblers are available. Everyone wit...1193 days ago
Bookmarks
shovill: Assemble bacterial isolate genomes from Illumina paired-end reads
...des at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Mega...1207 days ago
RNA-Seq De novo Assembly Using Trinity
...om paralogous genes. Briefly, the process works like so: Inchworm assembles the RNA-seq data into the un.... Build Trinity by typing 'make' in the base installation directory. Assemble RNA-Seq data like so: Trini...2953 days ago
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Pages
Genome Assembly Tools and Software - PART2 !!
...n VCF format, HAPCOMPASS will assemble reads into haplotypes. GAM-N...bsp;is not a standard de novo assembler. It aims “only”...ap graph-based de novo genome assembler. Omega 1.0.2 – Overla...nbsp;is a parallel short read assembler for large genomes using de B...2674 days ago
Top-level pages
Commercial and public next-gen-seq (NGS) software
...tistics for: reads, contigs and snps. Align/Assemble to a reference BFAST - Blat-l...rs are from CRIBI in Italy. Win/Linux. RMAP - Assembles 20 - 64 bp Illumina reads to...nome.ucla.edu/index.php/BFAST De novo Align/Assemble ABySS - Assembly By Short Seq...3507 days ago
Software packages for next gen sequence analysis
...Search - Fledgling commercial product. Align/Assemble to a reference * BFAST - Blat...are from CRIBI in Italy. Win/Linux. * RMAP - Assembles 20 - 64 bp Illumina reads to...ports Illumina and SOLiD data. De novo Align/Assemble * ABySS - Assembly By Short S...3231 days ago
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Wire posts
Video
- https://genome10k.soe.ucsc.edu The Genome 10K project aims to assemble a genomic zoo—a collection of DNA sequences representing the genomes of 10,000 vertebrate species, approximately...
3556 days ago
- ...ere the process begins. Transcription factors assemble at a specific promoter region...ween the strands of the DNA double helix. The assembled collection of all these fact...for the synthesis of an RNA molecule which is assembled one sub-unit at a time by ma...
3372 days ago
Bio-Scripts
Palindrome Simulation commands !
...3326 cd masurca; ~/Tools/MaSuRCA-3.2.3/bin/masurca sim.conf 3327 ./assemble.sh 3328 cd .. 3329 ~/To...UT 3330 ~/Tools/platanus/platanus 3331 ~/Tools/platanus/platanus assemble 3332 ~/Tools/platanus/pla...1724 days ago
- Use pen and paper the assemble it. If you are brave enough, you can try to assemble this set of reads: CAGATGTCCT GACCTTTTCT TAAGATCTTT TCTTTAGCCG TTTCTTCTTT GAGCTTTACT TTACTTCATT T...
1203 days ago
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Tags
shovill: Assemble bacterial isolate genomes from Illumina paired-end reads
Shovill is a pipeline which uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill pr...Tags: shovill, Assemble, bacterial, isolate, genomes, Illumina, paired-end, reads
1207 days ago
- Recent technological progress has greatly facilitated de novo genome sequencing. However, de novo assemblies consist in many pieces of contiguous sequence (contigs) arranged in thousands of scaffolds instead of small numbers of chromosomes. Confirming and improving the quality...
Tags: Bioinformatics, Analysis, NGS, Stats, Assemble, Plot, TGNet, Visualize, Genome
2799 days ago
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Comments
Comment on "Short-read assembly using Spades !"
SPAdes (St. Petersburg genome assembler) is a popular tool for short-read assembly. It can assemble reads generated from Illumina, Ion...ir> with the name of the output directory where the assembled contigs will be saved. Ch...409 days ago
- ...ersion] [-citation] \ [-correct | -trim | -assemble | -trim-assemble] \ [-s <assembly-specifica...cted reads -trim - generate trimmed reads -assemble - generate an assembly -trim-...f the haploid genome size of what is being assembled. It is used primarily to est...
2087 days ago
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