NGMLR: long-read mapper designed to align PacBio or Oxford Nanopore
...ons for a read and then a banded Smith-Waterman alignment algorithm to compute the final alignment. Ngmlr us...penalizes gap extensions for longer gaps less than for shorter ones to compute precise alignments. The gap m...2211 days ago
“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
...into complete TE copies, including LTR-retrotransposon Retrieve corresponding TE sequences, and flanking sequences, from the local fasta files Compute summary statistics for each T...2172 days ago
FastANI: fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI)
...sp;Goris et al. 2007. However, it avoids expensive sequence alignments and uses Mashmap as its MinHash based sequence mapping engine to compute the orthologous mappings and...2132 days ago
2108 days ago
Snakemake—a scalable bioinformatics workflow engine
Snakemake is a workflow engine that provides a readable Python-based workflow definition language and a powerful execution environment that scales from single-core workstations to compute clusters without modifying the workflow.2081 days ago
GenomeThreader: Gene Prediction Software
GenomeThreader is a software tool to compute gene structure predictions. The gene structure predictions are calculated using a similarity-based approach where additional cDNA/EST...2050 days ago
QUAST-LG: Versatile genome assembly evaluation
...pares large genomic de novo assemblies against reference sequences and computes relevant quality metrics. Si...ncept of upper bound assembly for a given genome and set of reads, and compute theoretical limits on assembl...2028 days ago
MITOS: improved de novo metazoan mitochondrial genome annotation
Allows automatic annotation of metazoan mitochondrial genomes. MITOS is a pipeline designed to compute a consistent de novo annotation of the mitogenomic sequences. The software allow...2027 days ago
SKESA: strategic k-mer extension for scrupulous assemblies
...l contamination in reads, is fast, and produces an identical assembly for the same input when assembled multiple times with the same or different compute resources. Source code for...2008 days ago
1939 days ago