transrate: Understanding your transcriptome assembly
...ce such as the sequencing reads, reporting quality scores for contigs and assemblies. This allows you to choose between assemblers and parameters, filter out the bad contigs from an a...2120 days ago
BLAST options, setting and defaults
...ents:number of alignments to show (B) [integer] default = 15 default = 15 default = 15 default = 15 default = 15 default = 15 Query filter:filter applied to the query sequence...1970 days ago
The Extensive de novo TE Annotator (EDTA)
The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of i...1729 days ago
Shouji: a fast and efficient pre-alignment filter for sequence alignment
...bsp; We introduce Shouji, a highly parallel and accurate pre-alignment filter that remarkably reduces the n...rogramming algorithms. The first key idea of our proposed pre-alignment filter is to provide high filtering...1641 days ago
1563 days ago
MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization
MitoZ is a Python3-based toolkit which aims to automatically filter pair-end raw data (fastq files), assemble genome, search for mitogenome sequences from the genome assembly result,...1560 days ago
Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
...(default: not used) -stage INT: start from which stage (default: 0) 0-start from begining(storing kmers in bloom filter) ; 1-start from count kmers showed up in bloom filter; 2-start from dumping kmer...1548 days ago
Filtlong: quality filtering tool for long reads
Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a...and read identity (higher is better) when choosing which reads pass the filter. Filtlong builds into a stan...1450 days ago
1358 days ago
SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs
The first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. SneakySnake greatly (by more than two orders of ma...1229 days ago