2004 days ago
Genome assembly tutorial "Genome Assembly for short and long reads"
In this lab we will perform de novo genome assembly of a bacterial genome. You will be guided throug...erform basic quality checks on the input data How to run a short read assembler on Illumina data How to run a long read assem...1992 days ago
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 asse...e default is to use only clipped, discordant, unmapped and indel reads, although this can be customized to any set of reads at t...1990 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. The decector will break a c...the correct, unaffected contigs. https://nxrepair.readthedoc...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 obs...1980 days ago
wtdbg2: A fuzzy Bruijn graph approach to long noisy reads assembly
...e novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the con...utput. ./wtdbg2 -x rs -g 4.6m -t 16 -i reads.fa.gz -fo prefix ./wtpoa-cns -t 1...1976 days ago
SDA: Long-read sequence and assembly of segmental duplications
Segmental Duplication Assembler (SDA; https://github.com/mvollger/SDA) constructs grap...alogous sequence variants define the nodes and long-read sequences provide attraction...edges, enabling the partition and assembly of long reads corr...1947 days ago
ChIPulate: A Python3 framework to simulate read counts in a ChIP-seq experiment
ChIP-seq simulation pipeline, ChIPulate, we assess the impact of various biological and experimental sources of variation on several outcomes of a ChIP-seq experiment, vi...1927 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 is designed for a wide...package represents a complete pipeline: it takes raw PB / ONT reads as i...1919 days ago