1389 days ago
1326 days ago
CoverM: Read coverage calculator for metagenomics
...undance calculator focused on metagenomics applications. CoverM calculates coverage of genomes/MAGs coverm genome (help) or individual contigs coverm contig (help...1141 days ago
1247 days ago
AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads
AlignGraph2 is the second version of AlignGraph for PacBio long reads. It extends and refines contigs assembled from the long reads with a published genome similar to the sequencing genome. More at https://academic.oup.com/bib/advance-article-abstract/doi/10.1093/bib/bbab022/61467721188 days ago
916 days ago
UniqueKmer: Generate unique KMERs for every contig in a FASTA file
...that are only presented in one contig, but not presented in any other contigs (for both forward and reverse...ands). This tool accepts the input of a FASTA file consisting of many contigs, and extract unique k-mers fo...910 days ago
auN: a new metric to measure assembly contiguity
...e nor median. It is the length of the contig such that this and longer contigs cover at least 50% of the ass...indicates better contiguity. We can similarly define Nx such that contigs no shorter than Nx cover...682 days ago
HairSplitter: assembling long reads in an unknown number of haplotypes
...er: Very modular, can be used with any assembler Naive: makes no assumption on ploidy, parameter-free Safe: won’t artificially duplicate contigs HairSplitter splits...555 days ago
Orthoflow: workflow for phylogenetic inference of genome-scale datasets of protein-coding genes
...e-scale datasets of protein-coding genes. Our goal was to make it straightforward to work from a combination of input sources including annotated contigs in Genbank format and FASTA f...114 days ago