Tags: Bioinformatics, Analysis, Assembly, Genome, BRIG, Plot, View, BLAST
2651 days ago
Tags: Bioinformatics, Analysis, Assembly, Genome, bedtools, View, Alignment, BAM, SAM
2643 days ago
ConPADE: Genome Assembly Ploidy Estimation from Next-Generation Sequencing Data
ConPADE (Contig Ploidy and Allele Dosage Estimation), a probabilistic method that estimates the ploidy of any given contig/scaffold based on its allele proportions. In the process, they report findings regarding errors in sequencing. The method can be used for whole genome shotgun (WGS) sequencin...Tags: Bioinformatics, Analysis, Assembly, Genome, ConPADE, Polyploidy
2643 days ago
FinisherSC: a repeat-aware and scalable tool for upgrading de novo assembly using long reads
FinisherSC, a repeat-aware and scalable tool for upgrading de novo assembly using long reads. Experiments with real data suggest that FinisherSC can provide longer and higher quality contigs than existing tools while maintaining high concordance.Tags: Bioinformatics, Analysis, Assembly, Genome, PacBio, Long, FinisherSC
2640 days ago
PBSuite: Software for Long-Read Sequencing Data from PacBio
PBJelly - the genome upgrading tool. PBHoney - the structural variation discovery tool Both are contained within the PBSuite code found in downloads.----- PBJelly -----Read The Paper http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047768PBJelly is a highly autom...Tags: Bioinformatics, Analysis, Assembly, Genome, PacBio, Long, Improve, PBSuite, PBJelly, PBHoney
2640 days ago
splitbam: splits a BAM by chromosomes
splitbam splits a BAM by chromosomes. Using the reference sequence dictionary (*.dict), it also creates some empty BAM files if no sam record was found for a chromosome. A pair of 'mock' SAM-Records can also be added to those empty BAMs to avoid some tools (like samtools) to crash. Usage ...Tags: Bioinformatics, Analysis, Assembly, Genome, Split, Reads
2639 days ago
Tags: Bioinformatics, Analysis, Assembly, Genome, MyCC, Binning
2636 days ago
Tags: Bioinformatics, Analysis, Assembly, Genome, Reads, Multi-genome
2636 days ago
Prokka: tool for the rapid annotation of prokaryotic genomes
Prokka is a software tool for the rapid annotation of prokaryotic genomes. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems. It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately...Tags: Bioinformatics, Analysis, Assembly, Genome, Annotation, Prokaryotes
2633 days ago
Tags: Bioinformatics, Analysis, Assembly, Genome, Bin, Binning, Metagenomics
2633 days ago