BAUM – Improving Genome Assembly by Adaptive Unique Mapping and Local Overlap-Layout-Consensus
...each region in parallel. BAUM can: (1) perform reference-assisted assembly based on the genome of a close species; (2) or improve the results of existing assemblies that are obtained...2034 days ago
RopeBWT2: Incremental construction of FM-index for DNA sequences
...is an tool for constructing the FM-index for a collection of DNA sequences. It works by incrementally inserting one or multiple sequences into an existing pseudo-BWT position by positi...2034 days ago
COSINE: non-seeding method for mapping long noisy sequences
Third generation sequencing (TGS) are highly promising technologies but the long and noisy reads from TGS are difficult to align using existing algorithms. Here, we present COSINE, a conceptually new method designed specifically for aligning long reads contaminated by a high level of errors.2033 days ago
ALLHiC: Phasing and scaffolding polyploid genomes based on Hi-C data
The major problem of scaffolding polyploid genome is that Hi-C signals are frequently detected between allelic haplotypes and any existing stat of art Hi-C scaffolding program links th...1978 days ago
kallisto: a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data
...nbsp;kallisto is therefore not only fast, but also as accurate as existing quantification tools. In fact...reads, in many benchmarks kallisto significantly outperforms existing tools. kallisto is...1960 days ago
SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation
...tein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of...1947 days ago
Roary: the Pan Genome Pipeline
...ousands of samples, something which is computationally infeasible with existing methods, without compromising...ing 1 GB of RAM and a single processor. To perform this analysis using existing methods would take weeks and...1945 days ago
plumber:An R package that converts your existing R code to a web API
plumber allows you to create a REST API by merely decorating your existing R source code with special comments. Take a look at an example. # plumber.R #* Echo back the input #* @p...1894 days ago
MSAProbs - Parallel and accurate multiple sequence alignment
...d using the popular benchmarks: BAliBASE, PREFAB, SABmark and OXBENCH, MSAProbs achieves statistically significant accuracy improvements over the existing top performing aligners, incl...1776 days ago
Kalign: fast multiple sequence alignment program for biological sequences.
...nd output the alignment in clustal format: kalign -i BB11001.tfa -f clu -o out.clu Re-align sequences in an existing alignment: kalign -i BB11001.msf -o out.afa Reformat existing alignment: kalign -i BB11001...1662 days ago