1966 days ago
Genome assembly tutorial "Genome Assembly for short and long reads"
...ovo genome assembly of a bacterial genome. You will be guided through the genome assembly starting with data quality control, through to building contigs and analysis of the results....1948 days ago
SvABA: Genome-wide detection of structural variants and indels by local assembly
...g Graph Assembler) by Jared Simpson, and BWA-MEM by Heng Li. Contigs are assembled for every 25kb...t of reads at the command line using VariantBam rules. These contigs are then immediately aligned...1946 days ago
NxRepair: error correction in de novo assemblies using Nextera Mate Pair Reads
...r will break a contig at the site of an identified misassembly and will generate a new fasta file containing both the corrected contigs and the correct, unaffected contigs. https://nxrepair.readthedoc...1943 days ago
MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons
...re. It has also proved useful in detecting undocumented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a reference coding se...1919 days ago
Flye: Fast and accurate de novo assembler for single molecule sequencing reads
...ojects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. Flye also includes a special...1875 days ago
RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs
...bsp;bioRxiv 2019. RaGOO is a tool for coalescing genome assembly contigs into pseudochromosomes via mi...ne with SV calling takes ~2 minutes. Intact ordering and orienting of contigs. Chimeric contig correction...1860 days ago
Flye: Fast and accurate de novo assembler for single molecule sequencing reads
...ojects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. Flye also includes a special...1781 days ago
RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs
...bsp;bioRxiv 2019. RaGOO is a tool for coalescing genome assembly contigs into pseudochromosomes via mi...ne with SV calling takes ~2 minutes. Intact ordering and orienting of contigs. Misassembly correction GFF...1668 days ago
Minipolish: A tool for Racon polishing of miniasm assemblies
...s of polishing a miniasm assembly: Adding read depth information to contigs Fixing sequence truncation that can occur in Racon Adding circularising links to circular contigs if not already present (so th...1631 days ago