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...1989 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...1248 days ago
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...1263 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...3009 days ago
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...2729 days ago
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...3563 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...3286 days ago
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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...1779 days ago
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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...464 days ago
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