1991 days ago
SvABA: Genome-wide detection of structural variants and indels by local assembly
SvABA is a method for detecting structural variants in sequencing data using genome-wide local assemb...he default is to use only clipped, discordant, unmapped and indel reads, although this can be customized to any set of reads a...1989 days ago
NxRepair: error correction in de novo assemblies using Nextera Mate Pair Reads
NxRepair is a python module that automatically detects large structural errors in de novo assemblies using Nextera mate pair reads....1987 days ago
nQuire: A statistical framework for ploidy estimation using NGS short-read data
nQuire implements a set of commands to estimate ploidy level of individuals from species, where recent polyploidization occurred and intraspecific ploidy variation is o...1980 days ago
wtdbg2: A fuzzy Bruijn graph approach to long noisy reads assembly
Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and...utput. ./wtdbg2 -x rs -g 4.6m -t 16 -i reads.f...1976 days ago
MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons
MACSE aligns coding NT sequences with respect to their AA translation while allowing NT sequences to contain multi...shifts in public database sequences and in aligning next-generation sequencing reads/c...1962 days ago
SDA: Long-read sequence and assembly of segmental duplications
Segmental Duplication Assembler (SDA; https://github.com/mvollger/SDA) constructs graphs in which paralogous seque...de attraction and repulsion edges, enabling the partition and assembly of long reads c...1947 days ago
HipSTR: Haplotype inference and phasing for Short Tandem Repeats
HipSTR was specifically developed to deal with these errors in the hopes of obtaining more robust STR genotyp...on-scale sequencing data Employing a specialized hidden Markov model to align reads t...1944 days ago
OMTools: a software package for visualizing and processing optical mapping data
OMTools, an efficient and intuitive data processing and...on suite to handle and explore large-scale optical mapping profiles. OMTools includes mo...an accessible and convenient pipeline for optical mapping analyses. https://github.com...1923 days ago
Flye: Fast and accurate de novo assembler for single molecule sequencing reads
Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It...lies. The package represents a complete pipeline: it takes raw PB / ONT reads a...1918 days ago