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.... ./wtdbg2 -x rs -g 4.6m -t 16 -i reads.fa.gz -fo prefix ./wtpoa-cns...1972 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...eshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a reference c...1958 days ago
SDA: Long-read sequence and assembly of segmental duplications
Segmental Duplication Assembler (SDA; https://github.com/mvollger/SDA) constructs gra...ide attraction and repulsion edges, enabling the partition and assembly of long reads corresponding to distinct par...1943 days ago
HipSTR: Haplotype inference and phasing for Short Tandem Repeats
HipSTR was specifically developed to deal with these errors in the hopes of obta...ion-scale sequencing data Employing a specialized hidden Markov model to align reads to candidate alleles while ac...1940 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 Technologi...he package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished...1914 days ago
FLAS: fast and high throughput algorithm for PacBio long read self-correction.
FLAS, a wrapper algorithm of MECAT, to achieve high throughput long read self-correction while keeping MECAT's fast speed. FLAS finds additional alignments from MECAT prealigned long reads to improve the correction throughput, and removes misalignments for accuracy.1834 days ago
jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator
jackalope simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina and Pacifi...simulate single, paired-end, or mate-pair Illumina reads, as well as reads from Pacifi...1800 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 Technologi...he package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished...1820 days ago
LRSDAY: Long-read Sequencing Data Analysis for Yeasts
Long-read sequencing technologies have become increasingly popular in genome projects...Saccharomyces cerevisiae, has many isolates currently being sequenced with long reads.1768 days ago
Minipolish: A tool for Racon polishing of miniasm assemblies
Miniasm is a great long-read assembly tool: straight-forward, effective and very...rror rate – they are essentially made of stitched-together pieces of long reads. Racon is a great polis...1670 days ago