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usually bioinformatics tools

http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/

This directory contains applications for stand-alone use, built specifically for a Linux 64-bit machine. For help on the bigBed and bigWig applications see: http://genome.ucsc.edu/goldenPath/help/bigBed.html http://genome.ucsc.edu/goldenPath/help/bigWig.html View the file ‘FOOTER’ to see the usage statement for each of the applications. Name Last modified Size Description Parent Directory – FOOTER 12-Jun-2012 18:01 65K bedClip 12-Jun-2012 18:01 […]

LOCAS, a new NGS assembler particularly designed for low coverage assembly of eukaryotic genome

Next Generation Sequencing (NGS) is a frequently applied approach to detect sequence variationsbetween highly related genomes. Recent large-scale re-sequencing studies as the Human 1000 GenomesProject utilize NGS data of low coverage to afford sequencing of hundreds of individuals. Here, SNPsand micro-indels can be detected by applying an alignment-consensus approach. However,computational methods capable of […]

ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data

Description

ANNOVA is an efficient software tool to utilize update-to-date information to functionally annotategenetic variants detected from diverse genomes. Given a list of variants with chromosome, startposition, end position and observed nucleotides, ANNOVAR can identify whether SNPs or indels causeprotein coding changes and what is the amino acids that were changed, or identify variants […]

ABACAS: Algorithm Based Automatic Contiguation of Assembled Sequences

http://abacas.sourceforge.net/index.html

ABACAS is intended to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence.

ABACAS uses MUMmer to find alignment positions and identify syntenies of assembled contigs against the reference. The output is then processed to generate a pseudomolecule taking overlapping […]

ABBA: Assembly Boosted By Amino acid sequences

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ABBA: Assembly Boosted By Amino acid sequences

Contents

[hide] 1 Overview 2 Download 3 References 4 Acknowledgements

Overview

Assembly Boosted By Amino acid sequence is a comparative gene assembler, which uses amino acid sequences from predicted proteins to help build a better assembly. see the journal paper.

[…]

one command line for getting consensus sequences from bam file

samtools mpileup -uf ref.fa aln.bam | bcftools view -cg – | vcfutils.pl vcf2fq > cns.fq

Merging separate sequence and quality files to FASTQ

#!/usr/bin/perl -w use strict; use Bio::SeqIO; use Bio::Seq::Quality; use Getopt::Long; die “pass a fasta and a fasta-quality file\n” unless @ARGV; my ($seq_infile,$qual_infile) = (scalar @ARGV == 1) ?($ARGV[0], “$ARGV[0].qual”) : @ARGV; ## Create input objects for both a seq (fasta) and qual file my $in_seq_obj = Bio::SeqIO->new( -file => $seq_infile, -format => ‘fasta’, ); my […]

Converting FASTQ to FASTA QUAL files

#!/usr/bin/env perl # Convert a fastq to a fasta/qual combo using BioPerl, with some Linux commands use Bio::Perl; use Data::Dumper; use strict; use warnings; use threads; use Thread::Queue; use Getopt::Long; my $settings={}; $|=1; my %numSequences; # static for a subroutine exit(main()); sub main{ die(“Usage: $0 -i inputFastqFile [-n numCpus -q outputQualfile -f outputFastaFile]”) if(@ARGV<1); GetOptions($settings,(‘numCpus=s’,’input=s’,’qualOut=s’,’fastaOut=s’)); […]

ACEAssemblySplitter.py

#! /usr/bin/env python2.7 desc = “”” Split an ACE format assembly file into multiple single ACE files each with a single contig. The resulting ACE contig files are formatted so that they can be read by CodonCode (http://www.codoncode.com). $ ACEAssemblySplitter.py test.ace -s 2 -e 3 – prints the second and third contigs in the test.ace […]

sam 2 bam 格式文件处理

Use the built-in “samtools sort” command rather than a generic sort. Samtools sort works on BAM files so you should convert your alignments to BAM format using

samtools view -bS filename.sam > filename.bam samtools sort filename.bam sorted samtools index sorted.bam

This ofcourse assumes you have generated the SAM file using method (1).

The file “sorted.bam” […]

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usually bioinformatics tools

LOCAS, a new NGS assembler particularly designed for low coverage assembly of eukaryotic genome

ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data

ABACAS: Algorithm Based Automatic Contiguation of Assembled Sequences

ABBA: Assembly Boosted By Amino acid sequences

one command line for getting consensus sequences from bam file

Merging separate sequence and quality files to FASTQ

Converting FASTQ to FASTA QUAL files

ACEAssemblySplitter.py

sam 2 bam 格式文件处理

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