AMStat: display statistics of large sequence files from next generation sequencing projects
...linker and adaptor sequences, causing poor mapping. Apart from this SAMStat can be used to verify individual processing steps in large analysis pipelines....2019 days ago
pWhatsHap: a parallel, high-performance version of WhatsHap
Given the potential relevance of efficient haplotyping in several analysis pipelines, we have designed and engineered pWhatsHap, a parallel, high-performance version of Wha...2014 days ago
1988 days ago
OrthoANI: An improved algorithm and software for calculating average nucleotide identity
...rest without unfamiliar Command Line Environments. Moreover, the OAT_cmd command-line software can be integrated into preexisting bioinformatics pipelines.1986 days ago
ARCS: scaffolding genome drafts with linked reads
ARCS requires two input files: Draft assembly fasta file Interleaved linked reads file (Barcode sequence expected in the BX tag of the read header or in the form "@readname_barcode" ; Run Long Ranger basic on raw chromium reads to produce this interleaved file)1981 days ago
1981 days ago
gVolante: Completeness Assessment of Genome/Transcriptome Sequences
A brand-new web server, gVolante, which provides an online tool for (i) on-demand completeness assessment of sequence sets by means of the previously developed pipelines CEGMA and BUSCO and (ii) browsing pre-computed completeness scores for publicly available data in its database section1954 days ago
1945 days ago
geck: trio-based comparative benchmarking of variant calls
...e two independent Platinum Genome trios. We show that our method is able to estimate differential precision and recall between the two pipelines with 10−3uncertain...1828 days ago
MALVA: Genotyping by Mapping-free ALlele Detection of Known VAriants
...able to genotype multi-allelic SNPs and indels without mapping reads MALVA calls correctly more indels than the most widely adopted genotyping pipelines Mapping-free approaches are...1575 days ago