Cerulean: A hybrid assembly using high throughput short and long reads
Cerulean extends contigs assembled using short read datasets like Illumina paired-end reads using long reads like PacBio RS long reads. Cerulean v0.1 has been implemented with bacterial genomes in mind. The method is fully described in Deshpande, V., Fung, E. D., Pham, S., & Bafna, V. (...Tags: Cerulean, hybrid, assembly, short, long, reads, pacbio, nanopore
2152 days ago
Tags: assemblytics, delta, analyze, alignment, assembly, reference, genome, visualization
2143 days ago
SWALO: Scaffolding with assembly likelihood optimization
SWALO (scaffolding with assembly likelihood optimization) is a method for scaffolding based on likelihood of genome assemblies computed using generative models for sequencing. Please email your questions, comments, suggestions, and bug reports to atif.bd@gmail.com.Tags: SWALO, Scaffolding, assembly, likelihood, optimization
2137 days ago
ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly
With increased availability of de novo assembly algorithms, it is feasible to study entire transcriptomes of non-model organisms. While algorithms are available that are specifically designed for performing transcriptome assembly from high-throughput sequencing data, they are very memory-intensiv...Tags: ASplice, scalable, memory-efficient, algorithm, de novo, transcriptome, assembly
2124 days ago
Tags: ChopStitch, exon, annotation, splice, graph, transcriptome, assembly, whole, genome, sequencing
2124 days ago
transrate: Understanding your transcriptome assembly
Transrate is software for de-novo transcriptome assembly quality analysis. It examines your assembly in detail and compares it to experimental evidence such as the sequencing reads, reporting quality scores for contigs and assemblies. This allows you to choose between assemblers and par...Tags: transrate, Understanding, transcriptome, assembly, rna-seq
2114 days ago
Converting a VCF into a FASTA given some reference !
Samtools/BCFtools (Heng Li) provides a Perl script vcfutils.pl which does this, the function vcf2fq (lines 469-528) This script has been modified by others to convert InDels as well, e.g. this by David Eccles ./vcf2fq.pl -f <input.fasta> <all-site.vcf> ...Tags: Convert, VCF, FASTA, reference, genome, assembly, phase
2107 days ago
Nanopolis: polish a genome assembly
Software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more (see Nanopolish modules, below). Quickst...Tags: Nanopolis, polish, ONT, nanopore, genome, assembly, ngs
2101 days ago
FinisherSC:a repeat-aware tool for upgrading de novo assembly using long reads
Here is the command to run the tool: python finisherSC.py destinedFolder mummerPath If you are running on server computer and would like to use multiple threads, then the following commands can generate 20 threads to run FinisherSC. python finisherSC.py -par 20 destinedFolder mummerPath S...Tags: FinisherSC, repeat-aware, tool, upgrading, de novo, assembly, long, reads
2076 days ago