SiLiX: implements an ultra-efficient algorithm for the clustering of homologous sequences
...of a network. A very efficient algorithm, based on the Disjoint Sets Data Structure, allows the computation of sequence families with low time and space requirements. A pa...1963 days ago
IQ-TREE: Efficient software for phylogenomic inference
...er phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time IQ-TREE found higher likelih...1896 days ago
Shouji: a fast and efficient pre-alignment filter for sequence alignment
...te infrastructures. In this work, we explore the use of hardware/software co-design and hardware acceleration to significantly reduce the execution time of short sequence alignment,...1636 days ago
mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
mosdepth can output: per-base depth about 2x as fast samtools depth--about 25 minutes of CPU time for a 30X genome.mean per-window depth given a window size--as would be used for CN...1624 days ago
Google Colab : Google Colab is a free cloud service and now it supports free GPU!
...;https://google-colab.com/, it is really easy, on the top right corner click 'submit +'. The earlier you post the more visibility you will get over time1549 days ago
Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
...tor has an accuracy higher than or comparable to existing methods, including the only other method (SEECER) designed for RNA-seq reads, and is more time and memory efficient. With a...1544 days ago
Tadpole: an assembler, error-corrector, and read-extender
...rectTo extend reads by 50bp in each direction:tadpole.sh in=reads.fq out=extended.fq mode=extend el=50 er=50To error-correct and extend at the same time, using a kmer length of 62:ta...1544 days ago
1541 days ago
Best Practices for Variant Calling with the GATK
The presentations below were filmed during the March 2015 GATK Workshop, part of the BroadE Workshop series. At the time of this workshop, the current version of Broad’s Genome...1527 days ago
1520 days ago