BioStar
Bioinformatician
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Bioinformatics Services / CRO Services
Last updated 2313 days ago by RASA Life SciencesRASA is set to provide premium technical and scientific services in a form of solutions, product development and training. .We are also very proficient in providing the high quality Research & Development services in life science informatics...gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output
By Rahul Nayak 2234 days agogithub.com - gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines. They compare the performance of gapFinisher against two other published gap filling tools PBJelly and...LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data
By BioStar 2209 days agocsb5.github.io - LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or...FiNGS: Filters for Next Generation Sequencing
By Neel 1834 days agogithub.com - Key features Filters SNVs from any variant caller to remove false positives Calculates metrics based on BAM files and provides filtering not possible with other tools Fully user-configurable filtering (including which filters to use and their...-
My commonly used commands in Bioinformatics
Last updated 2781 days ago by Rahul NayakFYI, I've found it useful to use MUMmer to extract the specific changes that Racon makes, so I can evaluate them individually: minimap -t 24 assembly.fasta long_reads.fastq.gz | racon -t 24 long_reads.fastq.gz - assembly.fasta... Referee: Genome assembly quality scores
By Jit 2679 days agogwct.github.io - Modern genome sequencing technologies provide a succint measure of quality at each position in every read, however all of this information is lost in the assembly process. Referee summarizes the quality information from the reads that map to a site...jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator
By Abhimanyu Singh 2416 days agogithub.com - jackalope simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina and Pacific Biosciences (PacBio) platforms. It can either read reference genomes from FASTA files or simulate new ones. Genomic variants...Kevler: Reference-free variant discovery in large eukaryotic genomes
By Jit 2230 days agogithub.com - Welcome to kevlar, software for predicting de novo genetic variants without mapping reads to a reference genome! kevlar's k-mer abundance based method calls single nucleotide variants (SNVs), multinucleotide variants (MNVs),...shovill: Assemble bacterial isolate genomes from Illumina paired-end reads
By BioStar 1890 days agogithub.com - Shovill is a pipeline which uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take...COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
By Jit 3013 days agoftp.genomics.org.cn - An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE...
