BOL

Filter the suplementary alignments samtools view -F 2048 -bo out.bam in.bam Then try, it should fix the error.

NAR Genomics and Bioinformatics https://academic.oup.com/nargab accept tools and software 

Scientist-B at ILS https://www.ils.res.in/wp-content/uploads/2020/04/ILS_ADVT_SCIENTISTS_2020.pdf #Job #Scientist

Whole-genome homology maps attempt to identify the evolutionary relationships between and within multiple genomes. The term "syntenic" is often used to describe regions of multiple genomes that are believed to have evolved from the same region in an...

Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools.Commonly used biological software and...

medaka is a tool to create a consensus sequence from nanopore sequencing data. This task is performed using neural networks applied from a pileup of individual sequencing reads against a draft assembly. It outperforms graph-based methods...

Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by...

BBMap is a global aligner and does not do any clipping by default and allows low-identity alignments. With the -slow flag, it will allow even more mismatches. Also, if you are mapping to genomic sequence (containing introns) then you need a...

I recently came across bbmap. When to use it ?

GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. GRIDSS includes a genome-wide break-end assembler, as well as a structural variation caller for Illumina sequencing data. GRIDSS calls variants...

gapFinisher to process SSPACE-LongRead output to fill gaps after the scaffolding. gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command...

LR_Gapcloser is a gap closing tool using long reads from studied species. The long reads could be downloaed from public read archive database (for instance, NCBI SRA database ) or be your own data. Then they are fragmented and aligned to scaffolds...

Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the...

Learn Perl6 https://learnxinyminutes.com/docs/perl6/ #perl6 #Raku

Ten Simple Rules for a successful remote postdoc https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007809 #PostDoc #Remote

Bioinformatics jobs in Africa https://www.mncjobs.co.za/search-jobs/bioinformatics

Genome detective https://www.genomedetective.com/app/typingtool/virus/

SARS-CoV-2 SNP Calling pipeline https://github.com/DamienFr/CoV-homoplasy

UK Covid consortium https://www.cogconsortium.uk/data/